diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java index 3f5c6ad4a5..63f890a102 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -191,7 +191,7 @@ public class ZenodoAPIClient implements Serializable { * @throws MissingConceptDoiException */ public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException { - setDepositionId(concept_rec_id); + setDepositionId(concept_rec_id, 1); String json = "{}"; OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); @@ -253,9 +253,10 @@ public class ZenodoAPIClient implements Serializable { } - private void setDepositionId(String concept_rec_id) throws IOException, MissingConceptDoiException { + private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(), ZenodoModelList.class); + ZenodoModelList zenodoModelList = new Gson() + .fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); for (ZenodoModel zm : zenodoModelList) { if (zm.getConceptrecid().equals(concept_rec_id)) { @@ -263,16 +264,23 @@ public class ZenodoAPIClient implements Serializable { return; } } - - throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + if (zenodoModelList.size() == 0) + throw new MissingConceptDoiException( + "The concept record id specified was missing in the list of depositions"); + setDepositionId(concept_rec_id, page + 1); } - private String getPrevDepositions() throws IOException { + private String getPrevDepositions(String page) throws IOException { + OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); + HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder(); + urlBuilder.addQueryParameter("page", page); + String url = urlBuilder.build().toString(); + Request request = new Request.Builder() - .url(urlString) + .url(url) .addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers .addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token) .get() diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index 5a59bc0dfe..e10d0c500c 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -75,9 +75,14 @@ public class DHPUtils { final HttpGet req = new HttpGet(url); + log.info("MDStoreManager request: {}", req); + try (final CloseableHttpClient client = HttpClients.createDefault()) { try (final CloseableHttpResponse response = client.execute(req)) { final String json = IOUtils.toString(response.getEntity().getContent()); + + log.info("MDStoreManager response: {}", json); + final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); return Arrays .stream(mdstores) diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java index 99ce961aa8..df9202ed88 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java @@ -172,6 +172,61 @@ public class PromoteActionPayloadForGraphTableJobTest { } } + @Test + void shouldPromoteActionPayload_custom() throws Exception { + + Class rowClazz = Publication.class; + Class actionPayloadClazz = Result.class; + MergeAndGet.Strategy strategy = MergeAndGet.Strategy.MERGE_FROM_AND_GET; + + // given + Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz); + Path inputActionPayloadDir = createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz); + Path outputGraphTableDir = outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase()); + + // when + PromoteActionPayloadForGraphTableJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputGraphTablePath", + inputGraphTableDir.toString(), + "-graphTableClassName", + rowClazz.getCanonicalName(), + "-inputActionPayloadPath", + inputActionPayloadDir.toString(), + "-actionPayloadClassName", + actionPayloadClazz.getCanonicalName(), + "-outputGraphTablePath", + outputGraphTableDir.toString(), + "-mergeAndGetStrategy", + strategy.name(), + "--shouldGroupById", + "true" + }); + + // then + assertTrue(Files.exists(outputGraphTableDir)); + + List actualOutputRows = readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz) + .collectAsList() + .stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + + Publication p = actualOutputRows + .stream() + .map(o -> (Publication) o) + .filter(o -> "50|4ScienceCRIS::6a67ed3daba1c380bf9de3c13ed9c879".equals(o.getId())) + .findFirst() + .get(); + + assertNotNull(p.getMeasures()); + assertTrue(p.getMeasures().size() > 0); + + } + public static Stream promoteJobTestParams() { return Stream .of( diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json index f98ee4b78c..d98bfe98f1 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json @@ -17,4 +17,5 @@ {"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018243405,"id":"50|CSC_________::00019460865d6cc381b36076131a5bc1","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"Computer Science::Networking and Internet 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private String pmid; + + private String pmcId; + /** * the DOI */ @@ -122,7 +125,7 @@ public class PMArticle implements Serializable { /** * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. - * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. + * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. * The NLM journal title abbreviation is exported in the element. * * @return the pubmed Journal Extracted @@ -140,10 +143,11 @@ public class PMArticle implements Serializable { } /** - * English-language abstracts are taken directly from the published article. - * If the article does not have a published abstract, the National Library of Medicine does not create one, - * thus the record lacks the and elements. However, in the absence of a formally - * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. + * contains the entire title of the journal article. is always in English; + * those titles originally published in a non-English language and translated for are enclosed in square brackets. + * All titles end with a period unless another punctuation mark such as a question mark or bracket is present. + * Explanatory information about the title itself is enclosed in parentheses, e.g.: (author's transl). + * Corporate/collective authors may appear at the end of for citations up to about the year 2000. * * @return the extracted pubmed Title */ @@ -250,4 +254,14 @@ public class PMArticle implements Serializable { public List getGrants() { return grants; } + + + public String getPmcId() { + return pmcId; + } + + public PMArticle setPmcId(String pmcId) { + this.pmcId = pmcId; + return this; + } } diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala index 49a2716415..9102c12c43 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala @@ -98,6 +98,7 @@ class PMParser(xml: XMLEventReader) extends Iterator[PMArticle] { case "PMID" => currentArticle.setPmid(text.trim) case "ArticleId" => if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim) + if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(text.trim) case "Language" => currentArticle.setLanguage(text.trim) case "ISSN" => currentJournal.setIssn(text.trim) case "GrantID" => currentGrant.setGrantID(text.trim) diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 92ad22c573..24a1fa62b9 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -4,9 +4,12 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType} import eu.dnetlib.dhp.schema.oaf._ -import collection.JavaConverters._ +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.lang3.StringUtils +import collection.JavaConverters._ import java.util.regex.Pattern +import scala.collection.mutable.ListBuffer /** */ @@ -14,6 +17,9 @@ object PubMedToOaf { val SUBJ_CLASS = "keywords" + val OAI_HEADER = "oai:pubmedcentral.nih.gov:" + val OLD_PMC_PREFIX = "od_______267::" + val urlMap = Map( "pmid" -> "https://pubmed.ncbi.nlm.nih.gov/", "doi" -> "https://dx.doi.org/" @@ -50,6 +56,17 @@ object PubMedToOaf { null } + + def createOriginalOpenaireId(article:PMArticle) :String = { + if (StringUtils.isNotEmpty(article.getPmcId)) { + val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC","")}") + s"$OLD_PMC_PREFIX$md5" + } + else + null + + } + /** Create an instance of class extends Result * starting from OAF instanceType value * @@ -122,8 +139,9 @@ object PubMedToOaf { return null // MAP PMID into pid with classid = classname = pmid - val pidList: List[StructuredProperty] = List( - OafMapperUtils.structuredProperty( + val pidList = ListBuffer[StructuredProperty]() + + pidList += OafMapperUtils.structuredProperty( article.getPmid, PidType.pmid.toString, PidType.pmid.toString, @@ -131,7 +149,19 @@ object PubMedToOaf { ModelConstants.DNET_PID_TYPES, dataInfo ) - ) + + + if (StringUtils.isNotBlank(article.getPmcId)) + { + pidList += OafMapperUtils.structuredProperty( + article.getPmcId, + PidType.pmc.toString, + PidType.pmc.toString, + ModelConstants.DNET_PID_TYPES, + ModelConstants.DNET_PID_TYPES, + dataInfo + ) + } if (pidList == null) return null @@ -186,6 +216,7 @@ object PubMedToOaf { val urlLists: List[String] = pidList .map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue)) .filter(t => t._1.nonEmpty) + .toList .map(t => t._1 + t._2) if (urlLists != null) pubmedInstance.setUrl(urlLists.asJava) @@ -262,7 +293,14 @@ object PubMedToOaf { if (authors != null && authors.nonEmpty) result.setAuthor(authors.asJava) - result.setOriginalId(pidList.map(s => s.getValue).asJava) + + if (StringUtils.isNotEmpty(article.getPmcId)) { + val originalIDS = ListBuffer[String]() + originalIDS += createOriginalOpenaireId(article) + pidList.map(s => s.getValue).foreach(p =>originalIDS += p) + result.setOriginalId(originalIDS.asJava) + } else + result.setOriginalId(pidList.map(s => s.getValue).asJava) result.setId(article.getPmid) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java index d50c1d5f39..5736bd95ed 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.actionmanager.ror; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; import java.io.FileInputStream; import java.util.List; @@ -38,25 +39,20 @@ class GenerateRorActionSetJobTest { .readValue(IOUtils.toString(getClass().getResourceAsStream("ror_org.json")), RorOrganization.class); final List> aas = GenerateRorActionSetJob.convertRorOrg(r); - Assertions.assertEquals(3, aas.size()); + Assertions.assertEquals(1, aas.size()); assertEquals(Organization.class, aas.get(0).getClazz()); - assertEquals(Relation.class, aas.get(1).getClazz()); - assertEquals(Relation.class, aas.get(2).getClazz()); final Organization o = (Organization) aas.get(0).getPayload(); - final Relation r1 = (Relation) aas.get(1).getPayload(); - final Relation r2 = (Relation) aas.get(2).getPayload(); - assertEquals(o.getId(), r1.getSource()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertEquals(ModelConstants.IS_PARENT_OF, r1.getRelClass()); - assertEquals(ModelConstants.IS_CHILD_OF, r2.getRelClass()); + assertNotNull(o); + + assertNotNull(o.getCountry()); + assertEquals("AU", o.getCountry().getClassid()); + + assertNotNull(o.getLegalname()); + assertEquals("Mount Stromlo Observatory", o.getLegalname().getValue()); System.out.println(mapper.writeValueAsString(o)); - System.out.println(mapper.writeValueAsString(r1)); - System.out.println(mapper.writeValueAsString(r2)); - } @Test diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java index 7bd7baaea9..7fc80d1681 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/TransformationJobTest.java @@ -19,7 +19,9 @@ import org.apache.spark.sql.Encoder; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.apache.spark.util.LongAccumulator; -import org.junit.jupiter.api.*; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.DisplayName; +import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.io.TempDir; import org.mockito.junit.jupiter.MockitoExtension; @@ -50,7 +52,7 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test Date cleaner") void testDateCleaner() throws Exception { - DateCleaner dc = new DateCleaner(); + final DateCleaner dc = new DateCleaner(); assertEquals("1982-09-20", dc.clean("20/09/1982")); assertEquals("2002-09-20", dc.clean("20-09-2002")); assertEquals("2002-09-20", dc.clean("2002-09-20")); @@ -68,9 +70,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_zenodo.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -86,9 +88,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/zenodo_tr.xslt"); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -108,9 +110,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); + final XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -129,9 +131,9 @@ class TransformationJobTest extends AbstractVocabularyTest { mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX")); mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_omicsdi.xml"))); // We Load the XSLT transformation Rule from the classpath - XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); + final XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript); - MetadataRecord result = tr.call(mr); + final MetadataRecord result = tr.call(mr); // Print the record System.out.println(result.getBody()); @@ -140,7 +142,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)") - void transformTestITGv4OAIdatacite(@TempDir Path testDir) throws Exception { + void transformTestITGv4OAIdatacite(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -203,7 +206,8 @@ class TransformationJobTest extends AbstractVocabularyTest { @Test @DisplayName("Test TransformSparkJobNode.main") - void transformTest(@TempDir Path testDir) throws Exception { + void transformTest(@TempDir + final Path testDir) throws Exception { try (SparkSession spark = SparkSession.builder().config(sparkConf).getOrCreate()) { @@ -256,6 +260,25 @@ class TransformationJobTest extends AbstractVocabularyTest { } } + @Test + @DisplayName("Test Transform Single XML using cnr_explora_tr XSLTTransformator") + void testCnrExploraTransformSaxonHE() throws Exception { + + // We Set the input Record getting the XML from the classpath + final MetadataRecord mr = new MetadataRecord(); + + mr.setProvenance(new Provenance("openaire____::cnr_explora", "CNR ExploRA", "cnr_________")); + mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_cnr_explora.xml"))); + // We Load the XSLT transformation Rule from the classpath + final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt"); + + final MetadataRecord result = tr.call(mr); + + // Print the record + System.out.println(result.getBody()); + // TODO Create significant Assert + } + private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); final LongAccumulator la = new LongAccumulator(); diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml index 22da07e299..58a73ae5d3 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml @@ -195,7 +195,9 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution. + Delineation of the intimate details of the backbone conformation of pyridine nucleotide + coenzymes in aqueous solution. + 1173-9 @@ -473,7 +475,9 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake. + Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and + inhibition of their uptake. + 1338-43 @@ -657,7 +661,8 @@ Biochemical and biophysical research communications Biochem Biophys Res Commun - Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + 1349-56 @@ -1627,7 +1632,9 @@ Biochemical pharmacology Biochem Pharmacol - Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal amidase-esterase. + Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal + amidase-esterase. + 1517-21 @@ -2030,7 +2037,9 @@ Biochemical pharmacology Biochem Pharmacol - Radiochemical assay of glutathione S-epoxide transferase and its enhancement by phenobarbital in rat liver in vivo. + Radiochemical assay of glutathione S-epoxide transferase and its enhancement by + phenobarbital in rat liver in vivo. + 1569-72 @@ -2350,7 +2359,9 @@ Biochemical pharmacology Biochem Pharmacol - Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled beta-adrenergic antagonists. + Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled + beta-adrenergic antagonists. + 1651-8 @@ -2598,7 +2609,9 @@ Biochemical pharmacology Biochem Pharmacol - The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells. + The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP + concentration and on incorporation of 32Pi into ATP in rat fat cells. + 1659-62 @@ -2851,7 +2864,9 @@ Biochemical pharmacology Biochem Pharmacol - Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the presence of valinomycin. + Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the + presence of valinomycin. + 1701-5 @@ -3265,7 +3280,8 @@ EC 2.6.1.16 - Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + EC 2.7.- @@ -3324,7 +3340,9 @@ Glucosamine - Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + Glutamine-Fructose-6-Phosphate Transaminase + (Isomerizing) + metabolism @@ -3463,7 +3481,8 @@ Biochemical pharmacology Biochem Pharmacol - Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines. + Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines. + 1731-3 @@ -3696,7 +3715,9 @@ Biochemical pharmacology Biochem Pharmacol - Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central catecholaminergic neurons of the rat. + Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central + catecholaminergic neurons of the rat. + 1739-42 @@ -4602,12 +4623,19 @@ Arzneimittel-Forschung Arzneimittelforschung - [Biochemical studies on camomile components/III. In vitro studies about the antipeptic activity of (--)-alpha-bisabolol (author's transl)]. + [Biochemical studies on camomile components/III. In vitro studies about the antipeptic + activity of (--)-alpha-bisabolol (author's transl)]. + 1352-4 - (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol only occurs in case of direct contact. In case of a previous contact with the substrate, the inhibiting effect is lost. + (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not + caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 + percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol + only occurs in case of direct contact. In case of a previous contact with the substrate, the + inhibiting effect is lost. + @@ -4626,7 +4654,9 @@ English Abstract Journal Article - Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die antipeptische Wirkung des (-)-alpha-Bisabolols + Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die + antipeptische Wirkung des (-)-alpha-Bisabolols + Germany @@ -4753,12 +4783,37 @@ Arzneimittel-Forschung Arzneimittelforschung - [Demonstration of tumor inhibiting properties of a strongly immunostimulating low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + [Demonstration of tumor inhibiting properties of a strongly immunostimulating + low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS + carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a + N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + 1369-79 - A report is given on the recent discovery of outstanding immunological properties in BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) However this comparison is characterized by the fact that both substances exhibit two quite different (complementary) mechanisms of action. Leucocyte counts made after application of the said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with ifosfamide, the known suppression in the post-therapeutic interval usually found with standard cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow conclusions on the immunity status. Since IF can be taken as one of the most efficient cancerostatics--there is no other chemotherapeutic known up to now that has a more significant effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, the total amount of leucocytes and lymphocytes as well as their time behaviour was determined from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained numerical values clearly show that further research work on the prophylactic use of this substance seems to be necessary and very promising. + A report is given on the recent discovery of outstanding immunological properties in + BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS + carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent + LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 + percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under + otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development + of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent + LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. + (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) + However this comparison is characterized by the fact that both substances exhibit two quite + different (complementary) mechanisms of action. Leucocyte counts made after application of the + said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with + ifosfamide, the known suppression in the post-therapeutic interval usually found with standard + cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow + conclusions on the immunity status. Since IF can be taken as one of the most efficient + cancerostatics--there is no other chemotherapeutic known up to now that has a more significant + effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, + the total amount of leucocytes and lymphocytes as well as their time behaviour was determined + from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained + numerical values clearly show that further research work on the prophylactic use of this + substance seems to be necessary and very promising. + @@ -4778,7 +4833,11 @@ English Abstract Journal Article - Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten + Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung + kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. + Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen + N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten + Germany @@ -5016,7 +5075,20 @@ 1400-3 - The distribution of blood flow to the subendocardial, medium and subepicardial layers of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). Regional myocardial blood flow was determined by means of the particle distribution method. In normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a significantly higher flow rate compared with the subepicardial layers. In hypoxia induced vasodilation this transmural gradient of flow was persistent. In contrast a marked redistribution of regional flow was observed under pharmacologically induced vasodilation. The transmural gradient decreased. In contrast to some findings these experiments demonstrate that a considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by drugs. The differences observed for the intramural distribution pattern of flow under hypoxia and drug induced vasodilation support the hypothesis that this pattern reflects corresponding gradients of regional myocardial metabolism. + The distribution of blood flow to the subendocardial, medium and subepicardial layers + of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic + (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). + Regional myocardial blood flow was determined by means of the particle distribution method. In + normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a + significantly higher flow rate compared with the subepicardial layers. In hypoxia induced + vasodilation this transmural gradient of flow was persistent. In contrast a marked + redistribution of regional flow was observed under pharmacologically induced vasodilation. The + transmural gradient decreased. In contrast to some findings these experiments demonstrate that a + considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by + drugs. The differences observed for the intramural distribution pattern of flow under hypoxia + and drug induced vasodilation support the hypothesis that this pattern reflects corresponding + gradients of regional myocardial metabolism. + @@ -5185,4 +5257,151 @@ + + + 4917185 + + 1970 + 10 + 27 + + + 2018 + 11 + 13 + +
+ + 0003-6919 + + 19 + 6 + + 1970 + Jun + + + Applied microbiology + Appl Microbiol + + Bactericidal activity of a broad-spectrum illumination source. + + 1013-4 + + + + Several hours of exposure to Vita-Lite lamps, which have a unique spectral + distribution, give significant killing of cells of Staphylococcus aureus. + + + + + Himmelfarb + P + P + + + Scott + A + A + + + Thayer + P S + PS + + + eng + + Journal Article + +
+ + United States + Appl Microbiol + 7605802 + 0003-6919 + + IM + + + Bacteriological Techniques + instrumentation + + + Light + + + Radiation Effects + + + Serratia marcescens + growth & development + radiation effects + + + Staphylococcus + growth & development + radiation effects + + + Sterilization + + + + + + + 1970 + 6 + 1 + + + 1970 + 6 + 1 + 0 + 1 + + + 1970 + 6 + 1 + 0 + 0 + + + ppublish + + 4917185 + PMC376844 + + + + Photochem Photobiol. 1969 Jan;9(1):99-102 + + 4889809 + + + + Endocrinology. 1969 Dec;85(6):1218-21 + + 5347623 + + + + Arch Mikrobiol. 1956;24(1):60-79 + + 13327987 + + + + J Bacteriol. 1941 Sep;42(3):353-66 + + 16560457 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt new file mode 100644 index 0000000000..78b167fdef --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/cnr_explora_tr.xslt @@ -0,0 +1,214 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml new file mode 100644 index 0000000000..220c4ddbe8 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_cnr_explora.xml @@ -0,0 +1,57 @@ + + +
+ + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt index 4fd95554a3..74a75e46a7 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt @@ -1232,4 +1232,268 @@ dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-学術雑誌論文（査 dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-紀要論文（査読有り） dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-雑誌記事（査読有り） dnet:review_levels @=@ 0001 @=@ 原著論文（査読有り） -dnet:review_levels @=@ 0001 @=@ 査読論文 \ No newline at end of file +dnet:review_levels @=@ 0001 @=@ 査読論文 +cnr:institutes @=@ https://ror.org/00brf2d87 @=@ CDS001 +cnr:institutes @=@ https://ror.org/00brf2d87 @=@ IDASC - Istituto di Acustica e Sensoristica \"Orso Mario Corbino\" +cnr:institutes @=@ https://ror.org/006qkqr45 @=@ CDS002 +cnr:institutes @=@ https://ror.org/006qkqr45 @=@ IAMC - Istituto per l'ambiente marino costiero +cnr:institutes @=@ https://ror.org/054ye0e45 @=@ CDS003 +cnr:institutes @=@ https://ror.org/054ye0e45 @=@ IASI - Istituto di analisi dei sistemi ed informatica \"Antonio Ruberti\" +cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ CDS004 +cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ IAC - Istituto per le applicazioni del calcolo \"Mauro Picone\" +cnr:institutes @=@ https://ror.org/000sy1f36 @=@ CDS005 +cnr:institutes @=@ https://ror.org/000sy1f36 @=@ IASF - Istituto di astrofisica spaziale e fisica cosmica +cnr:institutes @=@ https://ror.org/00x5wpm25 @=@ CDS006 +cnr:institutes @=@ https://ror.org/00x5wpm25 @=@ IBAM - Istituto per i beni archeologici e monumentali +cnr:institutes @=@ https://ror.org/03eqeqg74 @=@ CDS007 +cnr:institutes @=@ https://ror.org/03eqeqg74 @=@ IBP - Istituto di biochimica delle proteine +cnr:institutes @=@ https://ror.org/041xzk838 @=@ CDS008 +cnr:institutes @=@ https://ror.org/041xzk838 @=@ IBF - Istituto di biofisica +cnr:institutes @=@ https://ror.org/00s2j5046 @=@ CDS009 +cnr:institutes @=@ https://ror.org/00s2j5046 @=@ IBFM - Istituto di bioimmagini e fisiologia molecolare +cnr:institutes @=@ __CDS010__ @=@ CDS010 +cnr:institutes @=@ __CDS010__ @=@ IBAF - Istituto di biologia agro-ambientale e forestale +cnr:institutes @=@ __CDS011__ @=@ CDS011 +cnr:institutes @=@ __CDS011__ @=@ IBC - Istituto di biologia cellulare +cnr:institutes @=@ https://ror.org/02e5sbe24 @=@ CDS012 +cnr:institutes @=@ https://ror.org/02e5sbe24 @=@ IBBA - Istituto di biologia e biotecnologia agraria +cnr:institutes @=@ https://ror.org/01nyatq71 @=@ CDS013 +cnr:institutes @=@ https://ror.org/01nyatq71 @=@ IBPM - Istituto di biologia e patologia molecolari +cnr:institutes @=@ https://ror.org/01dy2q607 @=@ CDS014 +cnr:institutes @=@ https://ror.org/01dy2q607 @=@ IBIM - Istituto di biomedicina e di immunologia molecolare \"Alberto Monroy\" +cnr:institutes @=@ https://ror.org/05nzf7q96 @=@ CDS015 +cnr:institutes @=@ https://ror.org/05nzf7q96 @=@ IBIOM - Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari +cnr:institutes @=@ https://ror.org/05m1yqp60 @=@ CDS016 +cnr:institutes @=@ https://ror.org/05m1yqp60 @=@ IBIMET - Istituto di biometeorologia +cnr:institutes @=@ https://ror.org/03rqtqb02 @=@ CDS017 +cnr:institutes @=@ https://ror.org/03rqtqb02 @=@ IBB - Istituto di biostrutture e bioimmagini +cnr:institutes @=@ https://ror.org/04r5fge26 @=@ CDS018 +cnr:institutes @=@ https://ror.org/04r5fge26 @=@ ICAR - Istituto di calcolo e reti ad alte prestazioni +cnr:institutes @=@ https://ror.org/03wyf0g15 @=@ CDS019 +cnr:institutes @=@ https://ror.org/03wyf0g15 @=@ ICB - Istituto di chimica biomolecolare +cnr:institutes @=@ https://ror.org/02fkw1114 @=@ CDS020 +cnr:institutes @=@ https://ror.org/02fkw1114 @=@ ICCOM - Istituto di chimica dei composti organo metallici +cnr:institutes @=@ https://ror.org/0141vn777 @=@ CDS021 +cnr:institutes @=@ https://ror.org/0141vn777 @=@ ICRM - Istituto di chimica del riconoscimento molecolare +cnr:institutes @=@ __CDS022__ @=@ CDS022 +cnr:institutes @=@ __CDS022__ @=@ ICTP - Istituto di chimica e tecnologia dei polimeri +cnr:institutes @=@ __CDS023__ @=@ CDS023 +cnr:institutes @=@ __CDS023__ @=@ ICIS - Istituto di chimica inorganica e delle superfici +cnr:institutes @=@ https://ror.org/00be3zh53 @=@ CDS024 +cnr:institutes @=@ https://ror.org/00be3zh53 @=@ ISASI - Istituto di Scienze Applicate e Sistemi Intelligenti \"Eduardo Caianiello\" +cnr:institutes @=@ __CDS025__ @=@ CDS025 +cnr:institutes @=@ __CDS025__ @=@ ICEVO - Istituto di Studi sulle Civiltà dell'Egeo e del Vicino Oriente +cnr:institutes @=@ https://ror.org/02ynrme92 @=@ CDS026 +cnr:institutes @=@ https://ror.org/02ynrme92 @=@ ICVBC - Istituto per la conservazione e valorizzazione dei beni culturali +cnr:institutes @=@ https://ror.org/05wba8r86 @=@ CDS027 +cnr:institutes @=@ https://ror.org/05wba8r86 @=@ IC - Istituto di cristallografia +cnr:institutes @=@ https://ror.org/03z58xd74 @=@ CDS028 +cnr:institutes @=@ https://ror.org/03z58xd74 @=@ IDPA - Istituto per la dinamica dei processi ambientali +cnr:institutes @=@ https://ror.org/00n4jbh84 @=@ CDS029 +cnr:institutes @=@ https://ror.org/00n4jbh84 @=@ IEIIT - Istituto di elettronica e di ingegneria dell'informazione e delle telecomunicazioni +cnr:institutes @=@ https://ror.org/04sn06036 @=@ CDS030 +cnr:institutes @=@ https://ror.org/04sn06036 @=@ IEOS - Istituto per l'endocrinologia e l'oncologia \"Gaetano Salvatore\" +cnr:institutes @=@ https://ror.org/01rg40y89 @=@ CDS031 +cnr:institutes @=@ https://ror.org/01rg40y89 @=@ ICMATE - Istituto di Chimica della Materia Condensata e di Tecnologie per l'Energia +cnr:institutes @=@ https://ror.org/00dqega85 @=@ CDS032 +cnr:institutes @=@ https://ror.org/00dqega85 @=@ IFAC - Istituto di fisica applicata \"Nello Carrara\" +cnr:institutes @=@ https://ror.org/02n2bgz18 @=@ CDS033 +cnr:institutes @=@ https://ror.org/02n2bgz18 @=@ IFP - Istituto di fisica del plasma \"Piero Caldirola\" +cnr:institutes @=@ __CDS034__ @=@ CDS034 +cnr:institutes @=@ __CDS034__ @=@ IFSI - Istituto di fisica dello spazio interplanetario +cnr:institutes @=@ https://ror.org/01kdj2848 @=@ CDS035 +cnr:institutes @=@ https://ror.org/01kdj2848 @=@ IFC - Istituto di fisiologia clinica +cnr:institutes @=@ https://ror.org/049ebw417 @=@ CDS036 +cnr:institutes @=@ https://ror.org/049ebw417 @=@ IFN - Istituto di fotonica e nanotecnologie +cnr:institutes @=@ https://ror.org/01f5tnx94 @=@ CDS037 +cnr:institutes @=@ https://ror.org/01f5tnx94 @=@ IGI - Istituto gas ionizzati +cnr:institutes @=@ __CDS038__ @=@ CDS038 +cnr:institutes @=@ __CDS038__ @=@ IGP - Istituto di genetica delle popolazioni +cnr:institutes @=@ https://ror.org/04hadk112 @=@ CDS039 +cnr:institutes @=@ https://ror.org/04hadk112 @=@ IGB - Istituto di genetica e biofisica \"Adriano Buzzati Traverso\" +cnr:institutes @=@ https://ror.org/03qpd8w66 @=@ CDS040 +cnr:institutes @=@ https://ror.org/03qpd8w66 @=@ IGM - Istituto di genetica molecolare \"Luigi Luca Cavalli Sforza\" +cnr:institutes @=@ https://ror.org/01gtsa866 @=@ CDS041 +cnr:institutes @=@ https://ror.org/01gtsa866 @=@ IBBR - Istituto di Bioscienze e Biorisorse +cnr:institutes @=@ https://ror.org/00ytw6m58 @=@ CDS042 +cnr:institutes @=@ https://ror.org/00ytw6m58 @=@ IGAG - Istituto di geologia ambientale e geoingegneria +cnr:institutes @=@ https://ror.org/015bmra78 @=@ CDS043 +cnr:institutes @=@ https://ror.org/015bmra78 @=@ IGG - Istituto di geoscienze e georisorse +cnr:institutes @=@ https://ror.org/02gdcn153 @=@ CDS044 +cnr:institutes @=@ https://ror.org/02gdcn153 @=@ IIT - Istituto di informatica e telematica +cnr:institutes @=@ __CDS045__ @=@ CDS045 +cnr:institutes @=@ __CDS045__ @=@ ISIB - Istituto di ingegneria biomedica +cnr:institutes @=@ https://ror.org/05hky6p02 @=@ CDS046 +cnr:institutes @=@ https://ror.org/05hky6p02 @=@ IIA - Istituto sull'inquinamento atmosferico +cnr:institutes @=@ https://ror.org/011n2hw53 @=@ CDS047 +cnr:institutes @=@ https://ror.org/011n2hw53 @=@ ILIESI - Istituto per il lessico intellettuale europeo e storia delle idee +cnr:institutes @=@ https://ror.org/028g3pe33 @=@ CDS048 +cnr:institutes @=@ https://ror.org/028g3pe33 @=@ ILC - Istituto di linguistica computazionale \"Antonio Zampolli\" +cnr:institutes @=@ __CDS049__ @=@ CDS049 +cnr:institutes @=@ __CDS049__ @=@ IMAMOTER - Istituto per le macchine agricole e movimento terra +cnr:institutes @=@ https://ror.org/03m0n3c07 @=@ CDS050 +cnr:institutes @=@ https://ror.org/03m0n3c07 @=@ IMATI - Istituto di matematica applicata e tecnologie informatiche \"Enrico Magenes\" +cnr:institutes @=@ __CDS051__ @=@ CDS051 +cnr:institutes @=@ __CDS051__ @=@ IMCB - Istituto per i materiali compositi e biomedici +cnr:institutes @=@ https://ror.org/00z8ws214 @=@ CDS052 +cnr:institutes @=@ https://ror.org/00z8ws214 @=@ IMEM - Istituto dei materiali per l'elettronica ed il magnetismo +cnr:institutes @=@ __CDS053__ @=@ CDS053 +cnr:institutes @=@ __CDS053__ @=@ ISB - Istituto per i Sistemi Biologici +cnr:institutes @=@ https://ror.org/00bc51d88 @=@ CDS054 +cnr:institutes @=@ https://ror.org/00bc51d88 @=@ NANOTEC - Istituto di Nanotecnologia +cnr:institutes @=@ https://ror.org/024ye7w89 @=@ CDS055 +cnr:institutes @=@ https://ror.org/024ye7w89 @=@ IMAA - Istituto di metodologie per l'analisi ambientale +cnr:institutes @=@ __CDS056__ @=@ CDS056 +cnr:institutes @=@ __CDS056__ @=@ IMGC - Istituto di metrologia \"Gustavo Colonnetti\" +cnr:institutes @=@ https://ror.org/05vk2g845 @=@ CDS057 +cnr:institutes @=@ https://ror.org/05vk2g845 @=@ IMM - Istituto per la microelettronica e microsistemi +cnr:institutes @=@ https://ror.org/02qwy8e97 @=@ CDS058 +cnr:institutes @=@ https://ror.org/02qwy8e97 @=@ IM - Istituto motori +cnr:institutes @=@ __CDS059__ @=@ CDS059 +cnr:institutes @=@ __CDS059__ @=@ INMM - Istituto di neurobiologia e medicina molecolare +cnr:institutes @=@ https://ror.org/02dr63s31 @=@ CDS060 +cnr:institutes @=@ https://ror.org/02dr63s31 @=@ IRGB - Istituto di Ricerca Genetica e Biomedica +cnr:institutes @=@ https://ror.org/0240rwx68 @=@ CDS061 +cnr:institutes @=@ https://ror.org/0240rwx68 @=@ IN - Istituto di neuroscienze +cnr:institutes @=@ https://ror.org/02rzxrg25 @=@ CDS062 +cnr:institutes @=@ https://ror.org/02rzxrg25 @=@ OVI - Istituto opera del vocabolario italiano +cnr:institutes @=@ https://ror.org/05patmk97 @=@ CDS063 +cnr:institutes @=@ https://ror.org/05patmk97 @=@ IPCF - Istituto per i processi chimico-fisici +cnr:institutes @=@ __CDS064__ @=@ CDS064 +cnr:institutes @=@ __CDS064__ @=@ IPP - Istituto per la protezione delle piante +cnr:institutes @=@ https://ror.org/029st3z03 @=@ CDS065 +cnr:institutes @=@ https://ror.org/029st3z03 @=@ IRA - Istituto di radioastronomia +cnr:institutes @=@ https://ror.org/0040zx077 @=@ CDS066 +cnr:institutes @=@ https://ror.org/0040zx077 @=@ IRPI - Istituto di ricerca per la protezione idrogeologica +cnr:institutes @=@ https://ror.org/044bfsy89 @=@ CDS067 +cnr:institutes @=@ https://ror.org/044bfsy89 @=@ IRCRES - Istituto di Ricerca sulla Crescita Economica Sostenibile +cnr:institutes @=@ https://ror.org/01n1ayq61 @=@ CDS068 +cnr:institutes @=@ https://ror.org/01n1ayq61 @=@ IRPPS - Istituto di ricerche sulla popolazione e le politiche sociali +cnr:institutes @=@ https://ror.org/02db0kh50 @=@ CDS069 +cnr:institutes @=@ https://ror.org/02db0kh50 @=@ IRSA - Istituto di ricerca sulle acque +cnr:institutes @=@ https://ror.org/05813wx75 @=@ CDS070 +cnr:institutes @=@ https://ror.org/05813wx75 @=@ IRC - Istituto di ricerche sulla combustione +cnr:institutes @=@ https://ror.org/04vnwke91 @=@ CDS071 +cnr:institutes @=@ https://ror.org/04vnwke91 @=@ IRISS - Istituto di Ricerca su Innovazione e Servizi per lo Sviluppo +cnr:institutes @=@ https://ror.org/02wxw4x45 @=@ CDS072 +cnr:institutes @=@ https://ror.org/02wxw4x45 @=@ IREA - Istituto per il rilevamento elettromagnetico dell'ambiente +cnr:institutes @=@ https://ror.org/01j6drw72 @=@ CDS073 +cnr:institutes @=@ https://ror.org/01j6drw72 @=@ ISTEC - Istituto di scienza e tecnologia dei materiali ceramici +cnr:institutes @=@ https://ror.org/05kacka20 @=@ CDS074 +cnr:institutes @=@ https://ror.org/05kacka20 @=@ ISTI - Istituto di scienza e tecnologie dell'informazione \"Alessandro Faedo\" +cnr:institutes @=@ https://ror.org/00n8ttd98 @=@ CDS075 +cnr:institutes @=@ https://ror.org/00n8ttd98 @=@ ISAC - Istituto di scienze dell'atmosfera e del clima +cnr:institutes @=@ https://ror.org/0013zhk30 @=@ CDS076 +cnr:institutes @=@ https://ror.org/0013zhk30 @=@ ISA - Istituto di Scienze dell'Alimentazione +cnr:institutes @=@ https://ror.org/03x7xkr71 @=@ CDS077 +cnr:institutes @=@ https://ror.org/03x7xkr71 @=@ ISPA - Istituto di scienze delle produzioni alimentari +cnr:institutes @=@ https://ror.org/05w9g2j85 @=@ CDS078 +cnr:institutes @=@ https://ror.org/05w9g2j85 @=@ ISTC - Istituto di scienze e tecnologie della cognizione +cnr:institutes @=@ https://ror.org/032tyv240 @=@ CDS079 +cnr:institutes @=@ https://ror.org/032tyv240 @=@ ISTM - Istituto di scienze e tecnologie molecolari +cnr:institutes @=@ https://ror.org/02hdf6119 @=@ CDS080 +cnr:institutes @=@ https://ror.org/02hdf6119 @=@ ISMAR - Istituto di scienze marine +cnr:institutes @=@ https://ror.org/01yg57d71 @=@ CDS081 +cnr:institutes @=@ https://ror.org/01yg57d71 @=@ ISN - Istituto di scienze neurologiche +cnr:institutes @=@ https://ror.org/021z1mz76 @=@ CDS082 +cnr:institutes @=@ https://ror.org/021z1mz76 @=@ ISOF - Istituto per la sintesi organica e la fotoreattività +cnr:institutes @=@ https://ror.org/01wqae691 @=@ CDS083 +cnr:institutes @=@ https://ror.org/01wqae691 @=@ ISPAAM - Istituto per il sistema produzione animale in ambiente Mediterraneo +cnr:institutes @=@ __CDS084__ @=@ CDS084 +cnr:institutes @=@ __CDS084__ @=@ ISAFoM - Istituto per i sistemi agricoli e forestali del mediterraneo +cnr:institutes @=@ https://ror.org/00awwz417 @=@ CDS085 +cnr:institutes @=@ https://ror.org/00awwz417 @=@ ISPF - Istituto per la storia del pensiero filosofico e scientifico moderno +cnr:institutes @=@ https://ror.org/03a111314 @=@ CDS086 +cnr:institutes @=@ https://ror.org/03a111314 @=@ ISEM - Istituto di storia dell'Europa mediterranea +cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ CDS087 +cnr:institutes @=@ https://ror.org/01zz9wh30 @=@ ISM - Istituto di struttura della materia +cnr:institutes @=@ https://ror.org/035y5td47 @=@ CDS088 +cnr:institutes @=@ https://ror.org/035y5td47 @=@ ISGI - Istituto di studi giuridici internazionali +cnr:institutes @=@ __CDS089__ @=@ CDS089 +cnr:institutes @=@ __CDS089__ @=@ ISPRI - Istituto sperimentale di studi socio - economici sull'innovazione e le politiche della ricerca +cnr:institutes @=@ https://ror.org/051t1q308 @=@ CDS090 +cnr:institutes @=@ https://ror.org/051t1q308 @=@ ISSIA - Istituto di studi sui sistemi intelligenti per l'automazione +cnr:institutes @=@ https://ror.org/05k3cs357 @=@ CDS091 +cnr:institutes @=@ https://ror.org/05k3cs357 @=@ ISSIRFA - Istituto di studi sui sistemi regionali federali e sulle autonomie \"Massimo Severo Giannini\" +cnr:institutes @=@ https://ror.org/02gcxw165 @=@ CDS092 +cnr:institutes @=@ https://ror.org/02gcxw165 @=@ ISMA - Istituto di Studi sul Mediterraneo Antico +cnr:institutes @=@ https://ror.org/05db0es39 @=@ CDS093 +cnr:institutes @=@ https://ror.org/05db0es39 @=@ ISMed - Istituto di studi sul Mediterraneo +cnr:institutes @=@ https://ror.org/029k6t707 @=@ CDS094 +cnr:institutes @=@ https://ror.org/029k6t707 @=@ ISE - Istituto per lo studio degli ecosistemi +cnr:institutes @=@ https://ror.org/00w6r1881 @=@ CDS095 +cnr:institutes @=@ https://ror.org/00w6r1881 @=@ ISMN - Istituto per lo studio dei materiali nanostrutturati +cnr:institutes @=@ https://ror.org/01mfmr054 @=@ CDS096 +cnr:institutes @=@ https://ror.org/01mfmr054 @=@ ISMAC - Istituto per lo studio delle macromolecole +cnr:institutes @=@ https://ror.org/058nrs650 @=@ CDS097 +cnr:institutes @=@ https://ror.org/058nrs650 @=@ ITM - Istituto per la tecnologia delle membrane +cnr:institutes @=@ https://ror.org/0331xj092 @=@ CDS098 +cnr:institutes @=@ https://ror.org/0331xj092 @=@ ITABC - Istituto per le tecnologie applicate ai beni culturali +cnr:institutes @=@ https://ror.org/052q58629 @=@ CDS099 +cnr:institutes @=@ https://ror.org/052q58629 @=@ ITAE - Istituto di tecnologie avanzate per l'energia \"Nicola Giordano\" +cnr:institutes @=@ https://ror.org/04ehykb85 @=@ CDS100 +cnr:institutes @=@ https://ror.org/04ehykb85 @=@ ITB - Istituto di tecnologie biomediche +cnr:institutes @=@ https://ror.org/0221agg28 @=@ CDS101 +cnr:institutes @=@ https://ror.org/0221agg28 @=@ ITC - Istituto per le tecnologie della costruzione +cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ CDS102 +cnr:institutes @=@ https://ror.org/02xz4xc25 @=@ ITD - Istituto per le tecnologie didattiche +cnr:institutes @=@ __CDS103__ @=@ CDS103 +cnr:institutes @=@ __CDS103__ @=@ STIIMA - Istituto di Sistemi e Tecnologie Industriali Intelligenti per il Manifatturiero Avanzato +cnr:institutes @=@ https://ror.org/01as2bh37 @=@ CDS104 +cnr:institutes @=@ https://ror.org/01as2bh37 @=@ ITTIG - Istituto di teoria e tecniche dell'informazione giuridica +cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ CDS105 +cnr:institutes @=@ https://ror.org/01y5w6t76 @=@ ITOI - Istituto per i trapianti d'organo e immunocitologia +cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ CDS106 +cnr:institutes @=@ https://ror.org/04xy2mq71 @=@ IVALSA - Istituto per la valorizzazione del legno e delle specie arboree +cnr:institutes @=@ __CDS107__ @=@ CDS107 +cnr:institutes @=@ __CDS107__ @=@ IVV - Istituto di virologia vegetale +cnr:institutes @=@ https://ror.org/013nxtf56 @=@ CDS108 +cnr:institutes @=@ https://ror.org/013nxtf56 @=@ IRSIG - Istituto di ricerca sui sistemi giudiziari +cnr:institutes @=@ https://ror.org/05rcgef49 @=@ CDS109 +cnr:institutes @=@ https://ror.org/05rcgef49 @=@ ISC - Istituto dei sistemi complessi +cnr:institutes @=@ __CDS110__ @=@ CDS110 +cnr:institutes @=@ __CDS110__ @=@ INFM - Centro di responsabilità scientifica INFM +cnr:institutes @=@ https://ror.org/02dp3a879 @=@ CDS111 +cnr:institutes @=@ https://ror.org/02dp3a879 @=@ INO - Istituto nazionale di ottica +cnr:institutes @=@ __CDS112__ @=@ CDS112 +cnr:institutes @=@ __CDS112__ @=@ IDAIC - Centro di responsabilità di attività scientifica IDAIC +cnr:institutes @=@ https://ror.org/00p03yg71 @=@ CDS113 +cnr:institutes @=@ https://ror.org/00p03yg71 @=@ SPIN - Istituto superconduttori, materiali innovativi e dispositivi +cnr:institutes @=@ https://ror.org/00yfw2296 @=@ CDS114 +cnr:institutes @=@ https://ror.org/00yfw2296 @=@ IOM - Istituto officina dei materiali +cnr:institutes @=@ https://ror.org/0042e5975 @=@ CDS115 +cnr:institutes @=@ https://ror.org/0042e5975 @=@ NANO - Istituto Nanoscienze 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__CDS123__ @=@ ISPC - Istituto di Scienze del Patrimonio Culturale +cnr:institutes @=@ __CDS124__ @=@ CDS124 +cnr:institutes @=@ __CDS124__ @=@ IAS - Istituto per lo studio degli impatti Antropici e Sostenibilità in ambiente marino +cnr:institutes @=@ __CDS125__ @=@ CDS125 +cnr:institutes @=@ __CDS125__ @=@ IRET - Istituto di Ricerca sugli Ecosistemi Terrestri +cnr:institutes @=@ https://ror.org/03a0vt050 @=@ CDS126 +cnr:institutes @=@ https://ror.org/03a0vt050 @=@ ISTP - Istituto per la Scienza e Tecnologia dei Plasmi +cnr:institutes @=@ __CDS127__ @=@ CDS127 +cnr:institutes @=@ __CDS127__ @=@ ISP - Istituto di Scienze Polari +cnr:institutes @=@ https://ror.org/03byxpq91 @=@ CDS128 +cnr:institutes @=@ https://ror.org/03byxpq91 @=@ IRIB - Istituto per la Ricerca e l'Innovazione Biomedica +cnr:institutes @=@ __CDS129__ @=@ CDS129 +cnr:institutes @=@ __CDS129__ @=@ IGSG - Istituto di Informatica Giuridica e Sistemi Giudiziari +cnr:institutes @=@ __CDS130__ @=@ CDS130 +cnr:institutes @=@ __CDS130__ @=@ IBBC - Istituto di Biochimica e Biologia Cellulare +cnr:institutes @=@ __CDS131__ @=@ CDS131 +cnr:institutes @=@ __CDS131__ @=@ IBE - Istituto per la BioEconomia +cnr:institutes @=@ https://ror.org/0263zy895 @=@ CDS132 +cnr:institutes @=@ https://ror.org/0263zy895 @=@ SCITEC - Istituto di Scienze e Tecnologie Chimiche \"Giulio Natta\" +cnr:institutes @=@ __CDS133__ @=@ CDS133 +cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt index 93cc00eca4..0f0ebaad42 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt @@ -1077,4 +1077,137 @@ dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed -dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed \ No newline at end of file +dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00brf2d87 @=@ https://ror.org/00brf2d87 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/006qkqr45 @=@ https://ror.org/006qkqr45 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/054ye0e45 @=@ https://ror.org/054ye0e45 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/00ygy3d85 @=@ https://ror.org/00ygy3d85 +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/000sy1f36 @=@ https://ror.org/000sy1f36 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+cnr:institutes @=@ cnr:institutes @=@ __CDS130__ @=@ __CDS130__ +cnr:institutes @=@ cnr:institutes @=@ __CDS131__ @=@ __CDS131__ +cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ https://ror.org/0263zy895 +cnr:institutes @=@ cnr:institutes @=@ __CDS133__ @=@ __CDS133__ + diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 31784c7e92..68230b4778 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -2,11 +2,14 @@ package eu.dnetlib.dhp.datacite import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import org.apache.commons.io.FileUtils import org.apache.spark.SparkConf import org.apache.spark.sql.functions.{col, count} import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.{AfterEach, BeforeEach, Test} @@ -45,6 +48,9 @@ class DataciteToOAFTest extends AbstractVocabularyTest { } + + + @Test def testConvert(): Unit = { @@ -70,17 +76,18 @@ class DataciteToOAFTest extends AbstractVocabularyTest { assertEquals(100, nativeSize) - spark.read.load(targetPath).printSchema(); + val result: Dataset[String] = spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING) + + + - val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] result - .map(s => s.getClass.getSimpleName) .groupBy(col("value").alias("class")) .agg(count("value").alias("Total")) .show(false) - val t = spark.read.load(targetPath).count() + val t = spark.read.text(targetPath).as[String].count() assertTrue(t > 0) diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala new file mode 100644 index 0000000000..04d3c4a582 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala @@ -0,0 +1,31 @@ +package eu.dnetlib.dhp.datacite + +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse + +object DataciteUtilityTest { + + def convertToOAF(input:String) : String = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + + + val isRelation:String = (json \\ "source").extractOrElse("NULL") + + if (isRelation != "NULL") { + return "Relation" + } + + val iType: List[String] = for { + JObject(instance) <- json \\ "instance" + JField("instancetype", JObject(instancetype)) <- instance + JField("classname", JString(classname)) <- instancetype + + } yield classname + + val l:String =iType.head.toLowerCase() + l + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index ea742a04aa..b021e5e078 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -2,9 +2,10 @@ package eu.dnetlib.dhp.sx.bio import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} +import eu.dnetlib.dhp.schema.oaf.utils.PidType +import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result} import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved -import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PMSubject, PubMedToOaf} import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse @@ -16,6 +17,7 @@ import org.mockito.junit.jupiter.MockitoExtension import java.io.{BufferedReader, InputStream, InputStreamReader} import java.util.zip.GZIPInputStream import scala.collection.JavaConverters._ +import scala.collection.mutable.ListBuffer import scala.io.Source import scala.xml.pull.XMLEventReader @@ -72,6 +74,102 @@ class BioScholixTest extends AbstractVocabularyTest { ) println(mapper.writeValueAsString(r.head)) + } + + + private def checkPMArticle(article:PMArticle): Unit = { + assertNotNull(article.getPmid) + assertNotNull(article.getTitle) + assertNotNull(article.getAuthors) + article.getAuthors.asScala.foreach{a => + assertNotNull(a) + assertNotNull(a.getFullName) + } + + } + + @Test + def testParsingPubmedXML():Unit = { + val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val parser = new PMParser(xml) + parser.foreach(checkPMArticle) + } + + + private def checkPubmedPublication(o:Oaf): Unit = { + assertTrue(o.isInstanceOf[Publication]) + val p:Publication = o.asInstanceOf[Publication] + assertNotNull(p.getId) + assertNotNull(p.getTitle) + p.getTitle.asScala.foreach(t =>assertNotNull(t.getValue)) + p.getAuthor.asScala.foreach(a =>assertNotNull(a.getFullname)) + assertNotNull(p.getInstance()) + p.getInstance().asScala.foreach { i => + assertNotNull(i.getCollectedfrom) + assertNotNull(i.getPid) + assertNotNull(i.getInstancetype) + } + assertNotNull(p.getOriginalId) + p.getOriginalId.asScala.foreach(oId => assertNotNull(oId)) + + + val hasPMC = p.getInstance().asScala.exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString))) + + + + if (hasPMC) { + assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::"))) + } + } + + + @Test + def testPubmedOriginalID():Unit = { + val article:PMArticle = new PMArticle + + + article.setPmid("1234") + + article.setTitle("a Title") + + // VERIFY PUBLICATION IS NOT NULL + article.getPublicationTypes.add( new PMSubject("article",null, null)) + var publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] + assertNotNull(publication) + assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) + + // VERIFY PUBLICATION ID DOES NOT CHANGE ALSO IF SETTING PMC IDENTIFIER + article.setPmcId("PMC1517292") + publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication] + assertNotNull(publication) + assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId) + + // VERIFY ORIGINAL ID GENERATE IN OLD WAY USING PMC IDENTIFIER EXISTS + + + val oldOpenaireID ="od_______267::0000072375bc0e68fa09d4e6b7658248" + + val hasOldOpenAIREID = publication.getOriginalId.asScala.exists(o => o.equalsIgnoreCase(oldOpenaireID)) + + assertTrue(hasOldOpenAIREID) + } + + + @Test + def testPubmedMapping() :Unit = { + + val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))) + val parser = new PMParser(xml) + val results = ListBuffer[Oaf]() + parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies)) + + + + + results.foreach(checkPubmedPublication) + + + } @Test diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json new file mode 100644 index 0000000000..48a3777b79 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json @@ -0,0 +1,368 @@ + +{ + + "indexed": { + "date-parts": [ + [ + 2022, + 4, + 22 + ] + ], + "date-time": "2022-04-22T15:30:54Z", + "timestamp": 1650641454218 + }, + "reference-count": 31, + "publisher": "Cambridge University Press (CUP)", + "issue": "2", + "license": [ + { + "start": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ], + "date-time": "2017-08-22T00:00:00Z", + "timestamp": 1503360000000 + }, + "content-version": "unspecified", + "delay-in-days": 21, + "URL": "https://www.cambridge.org/core/terms" + } + ], + "content-domain": { + "domain": [ + + ], + "crossmark-restriction": false + }, + "short-container-title": [ + "Dance Res. J." + ], + "published-print": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + }, + "abstract": "Gaga, a practice developed by Israeli choreographer Ohad Naharin, is one of the most popular training methods on the global dance market. Structured as a metatechnique, or a system for negotiating techniques within one's body, Gaga teaches students to both draw on and reject multiple movement techniques to create their own movement. I consider how the paradigms of choreography, technique, and improvisation are blurred together in the pedagogical model of a metatechnique and how training dancers to shift between choreographer, dancer, and improviser has significant ramifications for understanding their agency. The metatechnique model of Gaga falls in line with neoliberal values of efficiency and a wide range of skills and knowledge; this analysis provides an understanding of recent trends in dance training in relation to contemporary political and socioeconomic structures.", + "DOI": "10.1017/s0149767717000183", + "type": "journal-article", + "created": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ], + "date-time": "2017-08-22T13:32:38Z", + "timestamp": 1503408758000 + }, + "page": "26-43", + "source": "Crossref", + "is-referenced-by-count": 10, + "title": [ + "Gaga as Metatechnique: Negotiating Choreography, Improvisation, and Technique in a Neoliberal Dance Market" + ], + "prefix": "10.1017", + "volume": "49", + "author": [ + { + "given": "Meghan", + "family": "Quinlan", + "sequence": "first", + "affiliation": [ + + ] + } + ], + "member": "56", + "published-online": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ] + }, + "reference": [ + { + "key": "S0149767717000183_ref22", + "first-page": "38", + "article-title": "‘I Don't Want to do African … What About My Technique?’: Transforming Dancing Places into Spaces in the Academy", + "volume": "4", + "author": "Monroe", + "year": "2011", + "journal-title": "The Journal of Pan African Studies" + }, + { + "key": "S0149767717000183_ref8", + "volume-title": "Discipline and Punish: The Birth of the Prison", + "author": "Foucault", + "year": "1995" + }, + { + "key": "S0149767717000183_ref24", + "volume-title": "Sharing the Dance: Contact Improvisation and American Culture", + "author": "Novack", + "year": "1990" + }, + { + "key": "S0149767717000183_ref26", + "doi-asserted-by": "publisher", + "DOI": "10.1215/9780822387879" + }, + { + "key": "S0149767717000183_ref10", + "doi-asserted-by": "publisher", + "DOI": "10.1080/01472526.2015.1085759" + }, + { + "key": "S0149767717000183_ref4", + "doi-asserted-by": "crossref", + "first-page": "235", + "volume-title": "Meaning in Motion", + "author": "Foster", + "year": "1997", + "DOI": "10.1215/9780822397281-013" + }, + { + "key": "S0149767717000183_ref17", + "doi-asserted-by": "publisher", + "DOI": "10.1093/acprof:oso/9780199360369.001.0001" + }, + { + "key": "S0149767717000183_ref30", + "volume-title": "The Precariat: The New Dangerous Class", + "author": "Standing", + "year": "2011" + }, + { + "key": "S0149767717000183_ref7", + "volume-title": "Choreographing Empathy: Kinesthesia in Performance", + "author": "Foster", + "year": "2011" + }, + { + "key": "S0149767717000183_ref14", + "volume-title": "A Brief History of Neoliberalism", + "author": "Harvey", + "year": "2007" + }, + { + "key": "S0149767717000183_ref27", + "unstructured": "Quinlan Meghan . 2016. “Gaga as Politics: A Case Study of Contemporary Dance Training.” PhD diss., University of California, Riverside." + }, + { + "key": "S0149767717000183_ref11", + "first-page": "xiii", + "volume-title": "Taken by Surprise: A Dance Improvisation Reader", + "author": "Gere", + "year": "2003" + }, + { + "key": "S0149767717000183_ref13", + "volume-title": "Declaration", + "author": "Hardt", + "year": "2012" + }, + { + "key": "S0149767717000183_ref29", + "doi-asserted-by": "publisher", + "DOI": "10.1057/9780230236844_9" + }, + { + "key": "S0149767717000183_ref5", + "doi-asserted-by": "publisher", + "DOI": "10.1057/9780230236844_6" + }, + { + "key": "S0149767717000183_ref28", + "doi-asserted-by": "publisher", + "DOI": "10.1017/S0149767700000528" + }, + { + "key": "S0149767717000183_ref12", + "doi-asserted-by": "publisher", + "DOI": "10.3998/mpub.287881" + }, + { + "key": "S0149767717000183_ref18", + "first-page": "135", + "volume-title": "Taken by Surprise: A Dance Improvisation Reader", + "author": "Marks", + "year": "2003" + }, + { + "key": "S0149767717000183_ref3", + "doi-asserted-by": "crossref", + "volume-title": "Bodies That Matter: On the Discursive Limits of Sex", + "author": "Butler", + "year": "2011", + "DOI": "10.4324/9780203828274" + }, + { + "key": "S0149767717000183_ref32", + "volume-title": "Choreographing Difference: The Body and Identity in Contemporary Dance", + "author": "Albright", + "year": "1997" + }, + { + "key": "S0149767717000183_ref16", + "doi-asserted-by": "publisher", + "DOI": "10.1017/S0149767714000163" + }, + { + "key": "S0149767717000183_ref15", + "doi-asserted-by": "publisher", + "DOI": "10.2307/1477803" + }, + { + "key": "S0149767717000183_ref21", + "first-page": "455", + "volume-title": "Incorporations", + "author": "Mauss", + "year": "1992" + }, + { + "key": "S0149767717000183_ref1", + "volume-title": "The Body Eclectic: Evolving Practices in Dance Training", + "author": "Bales", + "year": "2008" + }, + { + "key": "S0149767717000183_ref9", + "unstructured": "Gaga Movement Ltd. 2016. Gaga People. Dancers. Accessed June 28, 2016. http://gagapeople.com/english/." + }, + { + "key": "S0149767717000183_ref19", + "volume-title": "Critical Moves: Dance Studies in Theory and Politics", + "author": "Martin", + "year": "1998" + }, + { + "key": "S0149767717000183_ref2", + "volume-title": "Undoing the Demos: Neoliberalism's Stealth Revolution", + "author": "Brown", + "year": "2015" + }, + { + "key": "S0149767717000183_ref20", + "doi-asserted-by": "publisher", + "DOI": "10.1162/DRAM_a_00214" + }, + { + "key": "S0149767717000183_ref6", + "doi-asserted-by": "publisher", + "DOI": "10.1215/01610775-2009-016" + }, + { + "key": "S0149767717000183_ref23", + "doi-asserted-by": "publisher", + "DOI": "10.1093/acprof:oso/9780190201661.001.0001" + }, + { + "key": "S0149767717000183_ref25", + "volume-title": "Flexible Citizenship: The Cultural Logics of Transnationality", + "author": "Ong", + "year": "1999" + } + ], + "container-title": [ + "Dance Research Journal" + ], + "original-title": [ + + ], + "language": "en", + "link": [ + { + "URL": "https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0149767717000183", + "content-type": "unspecified", + "content-version": "vor", + "intended-application": "similarity-checking" + } + ], + "deposited": { + "date-parts": [ + [ + 2020, + 10, + 16 + ] + ], + "date-time": "2020-10-16T01:00:32Z", + "timestamp": 1602810032000 + }, + "score": 1, + "resource": { + "primary": { + "URL": "https://www.cambridge.org/core/product/identifier/S0149767717000183/type/journal_article" + } + }, + "subtitle": [ + + ], + "short-title": [ + + ], + "issued": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + }, + "references-count": 31, + "journal-issue": { + "issue": "2", + "published-print": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + } + }, + "alternative-id": [ + "S0149767717000183" + ], + "URL": "http://dx.doi.org/10.1017/s0149767717000183", + "relation": { + + }, + "ISSN": [ + "0149-7677", + "1940-509X" + ], + "issn-type": [ + { + "value": "0149-7677", + "type": "print" + }, + { + "value": "1940-509X", + "type": "electronic" + } + ], + "subject": [ + "Visual Arts and Performing Arts" + ], + "published": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + } + } diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 78ed375c67..98b5b708e6 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -475,6 +475,31 @@ class CrossrefMappingTest { } + @Test + def testConvertFromCrossRef2OafIssue(): Unit = { + val json = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_nojournal.json")) + .mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Publication]) + + assert(items.nonEmpty) + assert(items.size == 1) + val pub: Publication = items.head.asInstanceOf[Publication] + + assertNotNull(pub.getJournal.getIssnPrinted) + assertNotNull(pub.getJournal.getIssnOnline) + assertNotNull(pub.getJournal.getName) + + } + @Test def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java index 1a0afb9811..982e8ea750 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; +import java.util.Objects; import java.util.Optional; import org.apache.commons.io.IOUtils; @@ -102,6 +103,7 @@ public class SparkBulkTagJob { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java new file mode 100644 index 0000000000..ee01597e75 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.bulktag.eosc; + +import java.io.Serializable; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class DatasourceMaster implements Serializable { + private String datasource; + private String master; + + public String getDatasource() { + return datasource; + } + + public void setDatasource(String datasource) { + this.datasource = datasource; + } + + public String getMaster() { + return master; + } + + public void setMaster(String master) { + this.master = master; + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java new file mode 100644 index 0000000000..e9b1d3cfd8 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java @@ -0,0 +1,136 @@ + +package eu.dnetlib.dhp.bulktag.eosc; + +import java.io.BufferedWriter; +import java.io.Closeable; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.nio.charset.StandardCharsets; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.util.Arrays; +import java.util.List; +import java.util.function.Consumer; +import java.util.function.Function; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.DbClient; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.common.RelationInverse; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; + +public class ReadMasterDatasourceFromDB implements Closeable { + + private final DbClient dbClient; + private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class); + + private final BufferedWriter writer; + private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " + + "(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " + + "FULL JOIN " + + "(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " + + "ON dso.id = d.duplicate"; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + ReadMasterDatasourceFromDB.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json"))); + + parser.parseArgument(args); + + final String dbUrl = parser.get("postgresUrl"); + final String dbUser = parser.get("postgresUser"); + final String dbPassword = parser.get("postgresPassword"); + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("hdfsNameNode"); + + try ( + final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, + dbPassword)) { + + log.info("Processing datasources..."); + rmd.execute(QUERY, rmd::datasourceMasterMap); + + } + } + + public void execute(final String sql, final Function producer) { + + dbClient.processResults(sql, rs -> writeMap(producer.apply(rs))); + } + + public DatasourceMaster datasourceMasterMap(ResultSet rs) { + try { + DatasourceMaster dm = new DatasourceMaster(); + String datasource = rs.getString("datasource"); + dm.setDatasource(datasource); + String master = rs.getString("master"); + if (StringUtils.isNotBlank(master)) + dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true)); + else + dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true)); + return dm; + + } catch (final SQLException e) { + throw new RuntimeException(e); + } + } + + @Override + public void close() throws IOException { + dbClient.close(); + writer.close(); + } + + public ReadMasterDatasourceFromDB( + final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword) + throws IOException { + + this.dbClient = new DbClient(dbUrl, dbUser, dbPassword); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + } + + protected void writeMap(final DatasourceMaster dm) { + try { + writer.write(OBJECT_MAPPER.writeValueAsString(dm)); + writer.newLine(); + } catch (final IOException e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java new file mode 100644 index 0000000000..66e0c8af4f --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java @@ -0,0 +1,170 @@ + +package eu.dnetlib.dhp.bulktag.eosc; + +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import javax.print.attribute.DocAttributeSet; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.bulktag.SparkBulkTagJob; +import eu.dnetlib.dhp.bulktag.community.*; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; + +/** + * @author miriam.baglioni + * @Date 21/07/22 + */ +public class SparkEoscBulkTag implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscBulkTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + String datasourceMapPath = parser.get("datasourceMapPath"); + log.info("datasourceMapPath: {}", datasourceMapPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + Class resultClazz = (Class) Class.forName(resultClassName); + + SparkConf conf = new SparkConf(); + CommunityConfiguration cc; + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, workingPath); + execBulkTag(spark, inputPath, workingPath, datasourceMapPath, resultClazz); + }); + } + + private static void execBulkTag( + SparkSession spark, + String inputPath, + String workingPath, + String datasourceMapPath, + Class resultClazz) { + + List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) + .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) + .collectAsList(); + + readPath(spark, inputPath, resultClazz) + .map(patchResult(), Encoders.bean(resultClazz)) + .filter(Objects::nonNull) + .map( + (MapFunction) value -> enrich(value, hostedByList), + Encoders.bean(resultClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); + + readPath(spark, workingPath, resultClazz) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + + } + + private static R enrich(R value, List hostedByList) { + if (value + .getInstance() + .stream() + .anyMatch( + i -> (hostedByList.contains(i.getHostedby().getKey())) || + (value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)) + && + !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { + Context context = new Context(); + context.setId("eosc"); + context + .setDataInfo( + Arrays + .asList( + OafMapperUtils + .dataInfo( + false, BULKTAG_DATA_INFO_TYPE, true, false, + OafMapperUtils + .qualifier( + CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, + DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), + TAGGING_TRUST))); + value.getContext().add(context); + + } + return value; + + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + // TODO remove this hack as soon as the values fixed by this method will be provided as NON null + private static MapFunction patchResult() { + return r -> { + if (r.getDataInfo().getDeletedbyinference() == null) { + r.getDataInfo().setDeletedbyinference(false); + } + if (r.getContext() == null) { + r.setContext(new ArrayList<>()); + } + return r; + }; + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java similarity index 68% rename from dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java rename to dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java index b9de5dd111..7364966415 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java @@ -1,13 +1,10 @@ -package eu.dnetlib.dhp.bulktag; +package eu.dnetlib.dhp.bulktag.eosc; import static eu.dnetlib.dhp.PropagationConstant.readPath; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; -import java.util.function.Function; -import java.util.stream.Collectors; -import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -21,35 +18,11 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; public class SparkEoscTag { private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); - public static final Qualifier EOSC_QUALIFIER = OafMapperUtils - .qualifier( - "EOSC", - "European Open Science Cloud", - ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES); - public static final DataInfo EOSC_DATAINFO = OafMapperUtils - .dataInfo( - false, "propagation", true, false, - OafMapperUtils - .qualifier( - "propagation:subject", "Inferred by OpenAIRE", - ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), - "0.9"); - public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils - .structuredProperty( - "EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_GALAXY = OafMapperUtils - .structuredProperty( - "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); - public final static StructuredProperty EOSC_TWITTER = OafMapperUtils - .structuredProperty( - "EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -84,29 +57,35 @@ public class SparkEoscTag { }); } + public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics) { + EoscIfGuidelines eig = new EoscIfGuidelines(); + eig.setCode(code); + eig.setLabel(label); + eig.setUrl(url); + eig.setSemanticRelation(semantics); + return eig; + + } + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { readPath(spark, inputPath + "/software", Software.class) .map((MapFunction) s -> { - List sbject; - if (!Optional.ofNullable(s.getSubject()).isPresent()) - s.setSubject(new ArrayList<>()); - sbject = s.getSubject(); if (containsCriteriaNotebook(s)) { - sbject.add(EOSC_NOTEBOOK); - if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))) { - sbject = sbject.stream().map(sb -> { - if (sb.getValue().equals("EOSC Jupyter Notebook")) { - return null; - } - return sb; - }).filter(Objects::nonNull).collect(Collectors.toList()); - s.setSubject(sbject); - } + if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) + s.setEoscifguidelines(new ArrayList<>()); + addEIG( + s.getEoscifguidelines(), "EOSC::Jupyter Notebook", "EOSC::Jupyter Notebook", "", + "compliesWith"); + } if (containsCriteriaGalaxy(s)) { - sbject.add(EOSC_GALAXY); + if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent()) + s.setEoscifguidelines(new ArrayList<>()); + + addEIG( + s.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", "compliesWith"); } return s; }, Encoders.bean(Software.class)) @@ -123,15 +102,17 @@ public class SparkEoscTag { readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) .map((MapFunction) orp -> { - List sbject; - if (!Optional.ofNullable(orp.getSubject()).isPresent()) - orp.setSubject(new ArrayList<>()); - sbject = orp.getSubject(); + + if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent()) + orp.setEoscifguidelines(new ArrayList<>()); + if (containsCriteriaGalaxy(orp)) { - sbject.add(EOSC_GALAXY); + addEIG( + orp.getEoscifguidelines(), "EOSC::Galaxy Workflow", "EOSC::Galaxy Workflow", "", + "compliesWith"); } if (containscriteriaTwitter(orp)) { - sbject.add(EOSC_TWITTER); + addEIG(orp.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return orp; }, Encoders.bean(OtherResearchProduct.class)) @@ -148,12 +129,11 @@ public class SparkEoscTag { readPath(spark, inputPath + "/dataset", Dataset.class) .map((MapFunction) d -> { - List sbject; - if (!Optional.ofNullable(d.getSubject()).isPresent()) - d.setSubject(new ArrayList<>()); - sbject = d.getSubject(); + + if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent()) + d.setEoscifguidelines(new ArrayList<>()); if (containscriteriaTwitter(d)) { - sbject.add(EOSC_TWITTER); + addEIG(d.getEoscifguidelines(), "EOSC::Twitter Data", "EOSC::Twitter Data", "", "compliesWith"); } return d; }, Encoders.bean(Dataset.class)) @@ -169,6 +149,12 @@ public class SparkEoscTag { .json(inputPath + "/dataset"); } + private static void addEIG(List eoscifguidelines, String code, String label, String url, + String sem) { + if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code))) + eoscifguidelines.add(newInstance(code, label, url, sem)); + } + private static boolean containscriteriaTwitter(Result r) { Set words = getWordsSP(r.getTitle()); words.addAll(getWordsF(r.getDescription())); @@ -212,13 +198,6 @@ public class SparkEoscTag { return false; } - private static Set getSubjects(List s) { - Set subjects = new HashSet<>(); - s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" ")))); - s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase())); - return subjects; - } - private static Set getWordsSP(List elem) { Set words = new HashSet<>(); Optional @@ -242,9 +221,7 @@ public class SparkEoscTag { t -> words .addAll( Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); -// elem -// .forEach( -// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index 42b7804ea4..b9f3bff523 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Arrays; import java.util.List; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -87,6 +88,8 @@ public class PrepareDatasourceCountryAssociation { Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class) .filter( (FilterFunction) ds -> !ds.getDataInfo().getDeletedbyinference() && + Optional.ofNullable(ds.getDatasourcetype()).isPresent() && + Optional.ofNullable(ds.getDatasourcetype().getClassid()).isPresent() && (allowedtypes.contains(ds.getDatasourcetype().getClassid()) || whitelist.contains(ds.getId()))); diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json new file mode 100644 index 0000000000..9a2eadaa7d --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the name node on hdfs", + "paramRequired": true + }, + { + "paramName": "pgurl", + "paramLongName": "postgresUrl", + "paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb", + "paramRequired": true + }, + { + "paramName": "pguser", + "paramLongName": "postgresUser", + "paramDescription": "postgres user", + "paramRequired": false + }, + { + "paramName": "pgpasswd", + "paramLongName": "postgresPassword", + "paramDescription": "postgres password", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json new file mode 100644 index 0000000000..ebbbd408b5 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json @@ -0,0 +1,34 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "dmp", + "paramLongName":"datasourceMapPath", + "paramDescription": "the path where the association datasource master has been stored", + "paramRequired": true + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index f34c5110ff..9c1bbdf721 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -16,6 +16,21 @@ outputPath the output path + + + + postgresURL + the url of the postgress server to query + + + postgresUser + the username to access the postgres db + + + postgresPassword + the postgres password + + @@ -211,7 +226,7 @@ yarn-cluster cluster EOSC_tagging - eu.dnetlib.dhp.bulktag.SparkEoscTag + eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag dhp-enrichment-${projectVersion}.jar --num-executors=${sparkExecutorNumber} @@ -226,10 +241,132 @@ --sourcePath${outputPath} --workingPath${workingDir}/eoscTag - + + + + eu.dnetlib.dhp.bulktag.eosc.ReadMasterDatasourceFromDB + --hdfsPath${workingDir}/datasourcemaster + --hdfsNameNode${nameNode} + --postgresUrl${postgresURL} + --postgresUser${postgresUser} + --postgresPassword${postgresPassword} + + + + + + + + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/publication + --workingPath${workingDir}/eoscContextTag/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/dataset + --workingPath${workingDir}/eoscContextTag/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/software + --workingPath${workingDir}/eoscContextTag/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --datasourceMapPath${workingDir}/datasourcemaster + + + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${outputPath}/otherresearchproduct + --workingPath${workingDir}/eoscContextTag/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --datasourceMapPath${workingDir}/datasourcemaster + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java new file mode 100644 index 0000000000..cbdab7628a --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java @@ -0,0 +1,162 @@ + +package eu.dnetlib.dhp.bulktag; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/** + * @author miriam.baglioni + * @Date 22/07/22 + */ +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc +//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc +//"50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7" has two instance one hostedby eosc +//"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag + +public class EOSCContextTaggingTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCContextTaggingTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void EoscContextTagTest() throws Exception { + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + SparkEoscBulkTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input/dataset", + "-workingPath", workingDir.toString() + "/working/dataset", + "-datasourceMapPath", + getClass() + .getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster") + .getPath(), + "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + + Assertions + .assertEquals( + 1, + tmp + .filter( + d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") + && + d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) + .count()); + } + +} diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java index 1ea2541576..17e570fdf4 100644 --- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -1,21 +1,18 @@ package eu.dnetlib.dhp.bulktag; -import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; - import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.List; +import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag; import org.apache.commons.io.FileUtils; -import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.Row; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; @@ -126,10 +123,23 @@ public class EOSCTagJobTest { .assertEquals( 4, tmp + .filter(s -> s.getEoscifguidelines() != null) .filter( - s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) .count()); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions .assertEquals( 1, tmp @@ -140,6 +150,16 @@ public class EOSCTagJobTest { .size()); Assertions .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); + + Assertions + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() @@ -166,16 +186,24 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getEoscifguidelines() == null); + Assertions .assertEquals( - 9, tmp + 8, tmp .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) .collect() @@ -183,6 +211,23 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); Assertions .assertEquals( @@ -201,17 +246,24 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getEoscifguidelines() == null); Assertions .assertEquals( - 9, tmp + 8, tmp .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) .collect() @@ -219,14 +271,31 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions + .assertEquals( + 1, + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook"))); List subjects = tmp .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) .collect() .get(0) .getSubject(); - Assertions.assertEquals(8, subjects.size()); - Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertEquals(7, subjects.size()); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation"))); Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire"))); @@ -250,6 +319,17 @@ public class EOSCTagJobTest { .filter( ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) .count()); + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook"))) + .count()); Assertions .assertEquals( @@ -264,7 +344,22 @@ public class EOSCTagJobTest { .textFile(workingDir.toString() + "/input/otherresearchproduct") .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) .filter( - ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + orp -> orp + .getSubject() + .stream() + .anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); + + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + orp -> orp + .getSubject() + .stream() + .anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook"))) .count()); // spark.stop(); @@ -326,22 +421,41 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 1, + 0, tmp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines() != null) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getEoscifguidelines() != null) + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); Assertions .assertEquals( - 2, tmp + 1, tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( tmp .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) .collect() @@ -350,6 +464,24 @@ public class EOSCTagJobTest { .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))); + Assertions .assertEquals( 5, tmp @@ -385,22 +517,34 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 1, + 0, orp .filter( s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) .count()); + orp.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); Assertions .assertEquals( - 3, orp + 1, orp + .filter(o -> o.getEoscifguidelines() != null) + .filter( + o -> o + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow"))) + .count()); + + Assertions + .assertEquals( + 2, orp .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) .collect() .get(0) .getSubject() .size()); Assertions - .assertTrue( + .assertFalse( orp .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) .collect() @@ -408,6 +552,23 @@ public class EOSCTagJobTest { .getSubject() .stream() .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + Assertions + .assertEquals( + 1, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getEoscifguidelines() + .stream() + .anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow"))); Assertions .assertEquals( @@ -516,10 +677,20 @@ public class EOSCTagJobTest { Assertions .assertEquals( - 3, + 0, orp .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) .count()); + Assertions + .assertEquals( + 3, + orp + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) + .count()); JavaRDD dats = sc .textFile(workingDir.toString() + "/input/dataset") @@ -531,7 +702,11 @@ public class EOSCTagJobTest { .assertEquals( 3, dats - .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .filter( + s -> s + .getEoscifguidelines() + .stream() + .anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data"))) .count()); } diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json new file mode 100644 index 0000000000..63aa87e936 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json @@ -0,0 +1,10 @@ +{"author":[{"affiliation":[],"fullname":"Government of Alberta | Gouvernement de l'Alberta","name":"Government Of Alberta Gouvernement L.","pid":[],"rank":1,"surname":"Alberta"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::3795d6478e30e2c9f787d427ff160944","value":"Federated Research Data Repository / Dépôt fédéré de données de recherche"}],"context":[],"contributor":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Federated Research Data Repository"},{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Dépôt fédéré de données de recherche"}],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2013-05-28"},"dateofcollection":"2022-06-26T00:09:49+0000","dateoftransformation":"2022-06-26T01:48:37.716Z","description":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"The number of people who are unemployed as a percentage of the active labour force (i.e. employed and unemployed)."},{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Le nombre de personnes sans emploi en pourcentage de la population active (c'est-à-dire les personnes occupées et les chômeurs)."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"geolocation":[],"id":"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::3795d6478e30e2c9f787d427ff160944","value":"Federated Research Data Repository / Dépôt fédéré de données de 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+{"datasource":"eosc________::scigne::scigne.cloud_compute","master":"10|eosc________::7c63e3284c36b5977c553192dce506b3"} +{"datasource":"eosc________::scipedia::scipedia.scipedia","master":"10|eosc________::850abcddc76069f2c3c1cf77ad4beec9"} +{"datasource":"eosc________::scipedia::scipedia.topos_for_individuals","master":"10|eosc________::e6214b58f39a25b53eecda340f95ee7b"} +{"datasource":"eosc________::seadatanet::seadatanet.doi_minting_service","master":"10|eosc________::f87f72147a3c82c4f77684e40101e90e"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_marine_environmental_data_edmed","master":"10|eosc________::d79706389f0b864306feb47aac1f5766"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_marine_environmental_research_projects","master":"10|eosc________::baa9d2d6cdd8507fcbf76242e4c25d76"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_marine_organisations_edmo","master":"10|eosc________::5d23c66c26e0df209fc415c1e9ad0316"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_the_cruise_summary_reports_csr","master":"10|eosc________::fd70912c66037dc11f710587e281eeaf"} +{"datasource":"eosc________::seadatanet::seadatanet.european_directory_of_the_initial_ocean-observing_systems_edios","master":"10|eosc________::846016e987d1feaf2a36083f88dba1f2"} +{"datasource":"eosc________::seadatanet::seadatanet.seadatanet_cdi","master":"10|eosc________::36cd158d6b1bbdbfb443c68b8da00335"} +{"datasource":"eosc________::seadatanet::seadatanet.vocabulary_services_-_underpinned_by_the_nerc_vocabulary_server_nvs","master":"10|eosc________::4416d18ec7a57e553979fbfa4d862483"} +{"datasource":"eosc________::sinergise::sinergise.sentinel_hub","master":"10|eosc________::d36ae944fa207461bcb7b2b3a6c94de8"} +{"datasource":"eosc________::sixsq::sixsq.nuvla_multi-cloud_application_management_platform","master":"10|eosc________::38438cc3190a3815359efb53b9dd98eb"} +{"datasource":"eosc________::sks::sks.digital_production_for_conferences_workshops_roundtables_and_other_academic_and_professional_events","master":"10|eosc________::f6b51bef4a5f1478e980673339f2b2f3"} +{"datasource":"eosc________::smartsmear::smartsmear.smartsmear","master":"10|eosc________::d17a9325ca64ffad59e04659ed5404f7"} +{"datasource":"eosc________::sobigdata::sobigdata.tagme","master":"10|eosc________::0c3b8b80d9d6d38effd28bfa6a140a12"} +{"datasource":"eosc________::suite5::suite5.furniture_enterprise_analytics","master":"10|eosc________::29ed60070bd91bdc19c9f278b104465c"} +{"datasource":"eosc________::switch::switch.switchengines","master":"10|eosc________::d4143918a810115206640cfeb11e0ba6"} +{"datasource":"eosc________::t-systems::t-systems.open_telekom_cloud","master":"10|eosc________::c489ef6564a47922359f7b833919d642"} +{"datasource":"eosc________::terradue::terradue.eo_services_for_earthquake_response_and_landslides_analysis","master":"10|eosc________::ab3140d145deb5fdb02eeefbc5ebc471"} +{"datasource":"eosc________::tib::tib.open_research_knowledge_graph_orkg","master":"10|eosc________::ed6bd695c7a99297f360bc2fc915be90"} +{"datasource":"eosc________::ubora::ubora.ubora","master":"10|eosc________::bacf05aff1c6dcf3133a0352d5eb14c4"} +{"datasource":"eosc________::ubora::ubora.ubora_e-platform","master":"10|eosc________::947fde33605ba61216a07135ee1551f2"} +{"datasource":"eosc________::ugr-es::ugr-es.glacier_lagoons_of_sierra_nevada","master":"10|eosc________::8a966c0efca298ad5ec130d323c29935"} +{"datasource":"eosc________::uit::uit.dataverseno","master":"10|eosc________::92b76aa81a5b8443fcf17d3ae3c34211"} +{"datasource":"eosc________::uit::uit.the_troms_repository_of_language_and_linguistics_trolling","master":"10|fairsharing_::a36b0dcd1e6384abc0e1867860ad3ee3"} +{"datasource":"eosc________::ukaea::ukaea.prominence","master":"10|eosc________::06ce999c7cf77ea5a65f87bb563cd625"} +{"datasource":"eosc________::ukri_-_stfc::ukri_-_stfc.cvmfs_test","master":"10|eosc________::53aaa0a24d0edc47c23e722135c29dde"} +{"datasource":"eosc________::ukri_-_stfc::ukri_-_stfc.rucio","master":"10|eosc________::c19a8251c6bf563365c555572ace903e"} +{"datasource":"eosc________::uni-freiburg::uni-freiburg.european_galaxy_server","master":"10|eosc________::cc00fc2385475b80accec001dfb85efb"} +{"datasource":"eosc________::unibo::unibo.opencitations","master":"10|eosc________::573c29ecaf76ab961743bfc8a7d911ec"} +{"datasource":"eosc________::unifl::unifl.snap4city","master":"10|eosc________::9a55c40c3c082b7a8352ecbc56a87996"} +{"datasource":"eosc________::unige::unige.astronomical_online_data_analysis_astrooda","master":"10|eosc________::63f6119d3170cccf979daada3c5b524e"} +{"datasource":"eosc________::unitartu::unitartu.ut.rocket","master":"10|eosc________::da3450589a9d56212963b20cf729974c"} +{"datasource":"eosc________::upv-es::upv-es.lemonade","master":"10|eosc________::afdd227beada491f77d7944d7a0eafc9"} +{"datasource":"eosc________::vamdc::vamdc.portal","master":"10|eosc________::4dab2bb6e9a9ad223cd63c62c2ea804e"} +{"datasource":"eosc________::vamdc::vamdc.query_store","master":"10|eosc________::33f18bfe544c3c84ac28be6a3292d166"} +{"datasource":"eosc________::vamdc::vamdc.species_database","master":"10|eosc________::ae3587682dec5663a1b3b625036d15d0"} +{"datasource":"eosc________::vilnius-university::vilnius-university.the_national_open_access_research_data_archive_midas","master":"10|eosc________::4987ee0d071f68cf88f6b1a834b6733f"} +{"datasource":"eosc________::wenmr::wenmr.amber-based_portal_server_for_nmr_structures_amps-nmr","master":"10|eosc________::c6cca9747ef3ce296bd626bcbc4e480a"} +{"datasource":"eosc________::wenmr::wenmr.disvis_web_portal","master":"10|eosc________::2539ec693b683284c4e243b969ae3fc0"} +{"datasource":"eosc________::wenmr::wenmr.fanten_finding_anisotropy_tensor","master":"10|eosc________::99c793e3f3b856c48eaaa36682038b28"} +{"datasource":"eosc________::wenmr::wenmr.haddock24_web_portal","master":"10|eosc________::0f198f6a0885105809f420be23614be3"} +{"datasource":"eosc________::wenmr::wenmr.metalpdb","master":"10|eosc________::84676bc3d2ce17de70309dc58f428296"} +{"datasource":"eosc________::wenmr::wenmr.pdb-tools_web","master":"10|eosc________::b37eed45624ac30f3476f71640e59a61"} +{"datasource":"eosc________::wenmr::wenmr.powerfit_web_portal","master":"10|eosc________::93d4d621ed1da378c0e7dc891cefc007"} +{"datasource":"eosc________::wenmr::wenmr.spoton","master":"10|eosc________::76e7e0552f9c6b89db94b31ddc366b9f"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 87ac20948a..410feea02b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -10,6 +10,7 @@ import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -81,8 +82,9 @@ public class SparkPrepareResultProject implements Serializable { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY)); + Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index 6aed9d7a8c..34ca6697c4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -7,17 +7,22 @@ import java.io.Serializable; import java.util.List; import java.util.Objects; import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; /** @@ -33,87 +38,83 @@ public class SparkDumpFunderResults implements Serializable { SparkDumpFunderResults.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); - final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - - final String graphPath = parser.get("graphPath"); - log.info("relationPath: {}", graphPath); - SparkConf conf = new SparkConf(); - runWithSparkSession( conf, isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, graphPath); + writeResultProjectList(spark, inputPath, outputPath); }); } - private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String graphPath) { - - Dataset project = Utils - .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); - + private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) - .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - - List funderList = project - .select("id") - .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) - .distinct() - .collectAsList(); - + log.info("Number of result {}", result.count()); + Dataset tmp = result + .flatMap((FlatMapFunction) cr -> cr.getProjects().stream().map(p -> { + return getFunderName(p); + }).collect(Collectors.toList()).iterator(), Encoders.STRING()) + .distinct(); + List funderList = tmp.collectAsList(); funderList.forEach(funder -> { - String fundernsp = funder.substring(3); - String funderdump; - if (fundernsp.startsWith("corda")) { - funderdump = "EC_"; - if (fundernsp.endsWith("h2020")) { - funderdump += "H2020"; - } else { - funderdump += "FP7"; - } - } else { - funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); - } - writeFunderResult(funder, result, outputPath, funderdump); + dumpResults(funder, result, outputPath); }); - } - private static void dumpResults(String nsp, Dataset results, String outputPath, - String funderName) { + @NotNull + private static String getFunderName(Project p) { + Optional ofunder = Optional.ofNullable(p.getFunder()); + if (ofunder.isPresent()) { + String fName = ofunder.get().getShortName(); + if (fName.equalsIgnoreCase("ec")) { + fName += "_" + ofunder.get().getFundingStream(); + } + return fName; + } else { + String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase(); + if (fName.equalsIgnoreCase("ec")) { + if (p.getId().contains("h2020")) { + fName += "_H2020"; + } else { + fName += "_FP7"; + } + } else if (fName.equalsIgnoreCase("conicytf")) { + fName = "CONICYT"; + } else if (fName.equalsIgnoreCase("dfgf")) { + fName = "DFG"; + } else if (fName.equalsIgnoreCase("tubitakf")) { + fName = "TUBITAK"; + } else if (fName.equalsIgnoreCase("euenvagency")) { + fName = "EEA"; + } + return fName; + } + } + private static void dumpResults(String funder, Dataset results, String outputPath) { results.map((MapFunction) r -> { if (!Optional.ofNullable(r.getProjects()).isPresent()) { return null; } for (Project p : r.getProjects()) { - if (p.getId().startsWith(nsp)) { - if (nsp.startsWith("40|irb")) { - if (p.getFunder().getShortName().equals(funderName)) - return r; - else - return null; - } + String fName = getFunderName(p); + if (fName.equalsIgnoreCase(funder)) { return r; } } @@ -123,18 +124,6 @@ public class SparkDumpFunderResults implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath + "/" + funderName); + .json(outputPath + "/" + funder); } - - private static void writeFunderResult(String funder, Dataset results, String outputPath, - String funderDump) { - - if (funder.startsWith("40|irb")) { - dumpResults(funder, results, outputPath, "HRZZ"); - dumpResults(funder, results, outputPath, "MZOS"); - } else - dumpResults(funder, results, outputPath, funderDump); - - } - } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index d89b9e86dd..4b00729448 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -5,9 +5,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -18,11 +21,18 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; +import scala.Tuple2; /** * Selects the results linked to projects. Only for these results the dump will be performed. @@ -58,8 +68,10 @@ public class SparkResultLinkedToProject implements Serializable { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final String graphPath = parser.get("graphPath"); - log.info("graphPath: {}", graphPath); + final String resultProjectsPath = parser.get("graphPath"); + log.info("graphPath: {}", resultProjectsPath); + + String communityMapPath = parser.get("communityMapPath"); @SuppressWarnings("unchecked") Class inputClazz = (Class) Class.forName(resultClassName); @@ -70,43 +82,33 @@ public class SparkResultLinkedToProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, graphPath); + writeResultsLinkedToProjects( + communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath); }); } - private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String graphPath) { + private static void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark, + Class inputClazz, + String inputPath, String outputPath, String resultProjectsPath) { Dataset results = Utils .readPath(spark, inputPath, inputClazz) - .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); - Dataset relations = Utils - .readPath(spark, graphPath + "/relation", Relation.class) .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); - Dataset project = Utils.readPath(spark, graphPath + "/project", Project.class); - - results.createOrReplaceTempView("result"); - relations.createOrReplaceTempView("relation"); - project.createOrReplaceTempView("project"); - - Dataset tmp = spark - .sql( - "Select res.* " + - "from relation rel " + - "join result res " + - "on rel.source = res.id " + - "join project p " + - "on rel.target = p.id " + - "") - .as(Encoders.bean(inputClazz)); - tmp - .groupByKey( - (MapFunction) value -> value - .getId(), - Encoders.STRING()) - .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) + (FilterFunction) r -> !r.getDataInfo().getDeletedbyinference() && + !r.getDataInfo().getInvisible()); + Dataset resultProjectDataset = Utils + .readPath(spark, resultProjectsPath, ResultProject.class); + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + results + .joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId"))) + .map((MapFunction, CommunityResult>) t2 -> { + CommunityResult cr = (CommunityResult) ResultMapper + .map( + t2._1(), + communityMap, Constants.DUMPTYPE.FUNDER.getType()); + cr.setProjects(t2._2().getProjectsList()); + return cr; + }, Encoders.bean(CommunityResult.class)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java new file mode 100644 index 0000000000..38eb3cb370 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java @@ -0,0 +1,82 @@ + +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Objects; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +import scala.Tuple2; + +public class ProjectsSubsetSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + ProjectsSubsetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + final String projectListPath = parser.get("projectListPath"); + log.info("projectListPath: {}", projectListPath); + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + getNewProjectList(spark, inputPath, outputPath, projectListPath); + }); + } + + private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath, + String projectListPath) { + Dataset projectList = spark.read().textFile(projectListPath); + Dataset projects; + projects = Utils.readPath(spark, inputPath, Project.class); + projects + .joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left") + .map((MapFunction, Project>) t2 -> { + if (Optional.ofNullable(t2._2()).isPresent()) + return null; + return t2._1(); + }, Encoders.bean(Project.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + Utils + .readPath(spark, outputPath, Project.class) + .map((MapFunction) p -> p.getId(), Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(projectListPath); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 846440a696..e06327b2a2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -355,7 +355,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setPublisher(preparePublisher(doc, info)); r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); r.setSource(prepareSources(doc, info)); - r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); r.setFormat(prepareFormats(doc, info)); r.setContributor(prepareContributors(doc, info)); r.setResourcetype(prepareResourceType(doc, info)); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java index 6c72e4dfc4..ab6f54b92a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java @@ -65,11 +65,19 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl"); + log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl); + final String mdFormat = parser.get("mdFormat"); + log.info("mdFormat: {}", mdFormat); + final String mdLayout = parser.get("mdLayout"); + log.info("mdLayout: {}", mdLayout); + final String mdInterpretation = parser.get("mdInterpretation"); + log.info("mdInterpretation: {}", mdInterpretation); final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); final Set paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation); @@ -95,6 +103,8 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) .toArray(size -> new String[size]); + log.info("Processing existing paths {}", Arrays.asList(validPaths)); + if (validPaths.length > 0) { spark .read() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 5dc8e8910e..5669dca375 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -17,10 +17,10 @@ "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false }, -{ - "paramName": "gp", - "paramLongName": "graphPath", - "paramDescription": "the relationPath", - "paramRequired": true -} + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "the relationPath", + "paramRequired": false + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json new file mode 100644 index 0000000000..1a67134a6b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json @@ -0,0 +1,20 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index f5641bc456..6c45538cfe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -28,6 +28,12 @@ "paramLongName":"graphPath", "paramDescription": "the path to the relations", "paramRequired": true + }, + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the relations", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json new file mode 100644 index 0000000000..ed23136806 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json @@ -0,0 +1,27 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "pl", + "paramLongName": "projectListPath", + "paramDescription": "the path of the association result projectlist", + "paramRequired": true + } +] + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml similarity index 97% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml index e5ec3d0aee..d262cb6e05 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml @@ -27,4 +27,4 @@ oozie.launcher.mapreduce.user.classpath.first true - \ No newline at end of file + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml new file mode 100644 index 0000000000..619e3aa207 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml @@ -0,0 +1,171 @@ + + + + sourcePath + the source path + + + projectListPath + the path to the project list + + + outputPath + the output path + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/project + --resultTableNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${workingDir}/project + --communityMapPathnoneed + + + + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectsSubsetSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/project + --outputPath${workingDir}/tar/project + --projectListPath${projectListPath} + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/tar + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml deleted file mode 100644 index 5f954ff38a..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml +++ /dev/null @@ -1,347 +0,0 @@ - - - - - sourcePath - the source path - - - outputPath - the output path - - - communityMapPath - the path to the community map - - - selectedResults - the path the the possible subset ot results to be dumped - - - hiveDbName - the target hive database name - - - hiveJdbcUrl - hive server jdbc url - - - hiveMetastoreUris - hive server metastore URIs - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - oozieActionShareLibForSpark2 - oozie action sharelib for spark 2.* - - - spark2ExtraListeners - com.cloudera.spark.lineage.NavigatorAppListener - spark 2.* extra listeners classname - - - spark2SqlQueryExecutionListeners - com.cloudera.spark.lineage.NavigatorQueryListener - spark 2.* sql query execution listeners classname - - - spark2YarnHistoryServerAddress - spark 2.* yarn history server address - - - spark2EventLogDir - spark 2.* event log dir location - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - oozie.action.sharelib.for.spark - ${oozieActionShareLibForSpark2} - - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - yarn - cluster - Dump table publication for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/publication - --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication - --outputPath${workingDir}/dump/publication - --communityMapPath${communityMapPath} - --dumpType${dumpType} - - - - - - - - yarn - cluster - Dump table dataset for community/funder related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/dataset - --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset - --outputPath${workingDir}/dump/dataset - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table ORP for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/otherresearchproduct - --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct - --outputPath${workingDir}/dump/otherresearchproduct - --communityMapPath${communityMapPath} - - - - - - - - yarn - cluster - Dump table software for community related products - eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${selectedResults}/software - --resultTableNameeu.dnetlib.dhp.schema.oaf.Software - --outputPath${workingDir}/dump/software - --communityMapPath${communityMapPath} - - - - - - - - - - yarn - cluster - Prepare association result subset of project info - eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${sourcePath} - --outputPath${workingDir}/preparedInfo - - - - - - - - - - - - - - - yarn - cluster - Extend dumped publications with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/publication - --outputPath${outputPath}/ext/publication - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped dataset with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/dataset - --outputPath${outputPath}/ext/dataset - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped ORP with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/otherresearchproduct - --outputPath${outputPath}/ext/orp - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - yarn - cluster - Extend dumped software with information about project - eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - - --sourcePath${workingDir}/dump/software - --outputPath${outputPath}/ext/software - --preparedInfoPath${workingDir}/preparedInfo - - - - - - - - - - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt deleted file mode 100644 index 15387e988d..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml index 319517026a..dfbe93b672 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -77,42 +77,259 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${sourcePath} - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - + + + + + + + + + + yarn + cluster + Dump table publication for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${communityMapPath} + --dumpType${dumpType} + + + + + + + + yarn + cluster + Dump table dataset for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${workingDir}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/dataset + --outputPath${workingDir}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${workingDir}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/software + --outputPath${workingDir}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + - + yarn diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml index 8eab569928..7cc1333233 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -298,6 +298,7 @@ --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + --conf spark.sql.shuffle.partitions=3840 --sourcePath${sourcePath} --outputPath${workingDir}/validrelation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt deleted file mode 100644 index 15387e988d..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt +++ /dev/null @@ -1,2 +0,0 @@ -## This is a classpath-based import file (this header is required) -dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml index b990f4e49b..2c05256cf4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml @@ -77,12 +77,36 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + @@ -111,7 +135,8 @@ --sourcePath${sourcePath}/publication --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${workingDir}/result/publication - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -137,7 +162,8 @@ --sourcePath${sourcePath}/dataset --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${workingDir}/result/dataset - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -163,7 +189,8 @@ --sourcePath${sourcePath}/otherresearchproduct --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${workingDir}/result/otherresearchproduct - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} @@ -189,41 +216,14 @@ --sourcePath${sourcePath}/software --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${workingDir}/result/software - --graphPath${sourcePath} + --graphPath${workingDir}/preparedInfo + --communityMapPath${communityMapPath} - - - - - ${wf:appPath()}/dump_common - - - - - sourcePath - ${sourcePath} - - - selectedResults - ${workingDir}/result - - - communityMapPath - ${workingDir}/communityMap - - - outputPath - ${workingDir} - - - - - - + @@ -242,9 +242,8 @@ --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} - --sourcePath${workingDir}/ext + --sourcePath${workingDir}/result --outputPath${outputPath} - --graphPath${sourcePath} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json index 8bfdde5b0d..3a2f907089 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json @@ -1,5 +1,6 @@ [ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}, + {"paramName":"r", "paramLongName":"filterRelation", "paramDescription": "the relation to filter", "paramRequired": false} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json index 890570a0bd..cbb20bfe77 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/convert_object_json_params.json @@ -3,5 +3,7 @@ {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"su", "paramLongName":"scholixUpdatePath", "paramDescription": "the scholix updated Path", "paramRequired": false}, {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}, - {"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true} + {"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}, + {"paramName":"mp", "paramLongName":"maxPidNumberFilter", "paramDescription": "filter max number of pids in source/target", "paramRequired": false} + ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml new file mode 100644 index 0000000000..6fb2a1253c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/config-default.xml @@ -0,0 +1,10 @@ + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml new file mode 100644 index 0000000000..a37d85ad41 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/dumpScholix/oozie_app/workflow.xml @@ -0,0 +1,145 @@ + + + + sourcePath + the working dir base path + + + targetPath + the final graph path + + + relationFilter + Filter relation semantic + + + maxNumberOfPid + filter relation with at least #maxNumberOfPid + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Import JSONRDD to Dataset kryo + eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=3000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${sourcePath} + --targetPath${targetPath} + --filterRelation${relationFilter} + + + + + + + + + yarn + cluster + Convert Entities to summaries + eu.dnetlib.dhp.sx.graph.SparkCreateSummaryObject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=20000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/entities + --targetPath${targetPath}/provision/summaries + + + + + + + + yarn + cluster + Generate Scholix Dataset + eu.dnetlib.dhp.sx.graph.SparkCreateScholix + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=30000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --summaryPath${targetPath}/provision/summaries + --targetPath${targetPath}/provision/scholix + --relationPath${targetPath}/relation + + + + + + + + + + + + + + + + + yarn + cluster + Serialize scholix to JSON + eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=6000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${targetPath}/provision/scholix/scholix + --targetPath${targetPath}/json/scholix_json + --objectTypescholix + --maxPidNumberFiltermaxNumberOfPid + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala index bfa07eb69e..6695ebd3c8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertObjectToJson.scala @@ -4,6 +4,7 @@ import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.sx.scholix.Scholix import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary +import eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson.toInt import org.apache.commons.io.IOUtils import org.apache.hadoop.io.compress.GzipCodec import org.apache.spark.SparkConf @@ -12,6 +13,14 @@ import org.slf4j.{Logger, LoggerFactory} object SparkConvertObjectToJson { + def toInt(s: String): Option[Int] = { + try { + Some(s.toInt) + } catch { + case e: Exception => None + } + } + def main(args: Array[String]): Unit = { val log: Logger = LoggerFactory.getLogger(getClass) val conf: SparkConf = new SparkConf() @@ -37,6 +46,8 @@ object SparkConvertObjectToJson { log.info(s"objectType -> $objectType") val scholixUpdatePath = parser.get("scholixUpdatePath") log.info(s"scholixUpdatePath -> $scholixUpdatePath") + val maxPidNumberFilter = parser.get("maxPidNumberFilter") + log.info(s"maxPidNumberFilter -> $maxPidNumberFilter") implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix] implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] @@ -47,12 +58,22 @@ object SparkConvertObjectToJson { case "scholix" => log.info("Serialize Scholix") val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix] - val u: Dataset[Scholix] = spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix] - d.union(u) - .repartition(8000) - .map(s => mapper.writeValueAsString(s))(Encoders.STRING) - .rdd - .saveAsTextFile(targetPath, classOf[GzipCodec]) +// val u: Dataset[Scholix] = spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix] + if (maxPidNumberFilter != null && toInt(maxPidNumberFilter).isDefined) { + val mp = toInt(maxPidNumberFilter).get + d + .filter(s => (s.getSource.getIdentifier.size() <= mp) && (s.getTarget.getIdentifier.size() <= mp)) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .rdd + .saveAsTextFile(targetPath, classOf[GzipCodec]) + } else { + d + .repartition(8000) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .rdd + .saveAsTextFile(targetPath, classOf[GzipCodec]) + } + case "summary" => log.info("Serialize Summary") val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index bd970a5cf4..0073afff5e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -4,9 +4,11 @@ import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset} import org.apache.commons.io.IOUtils +import org.apache.commons.lang3.StringUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} + import scala.collection.JavaConverters._ object SparkConvertRDDtoDataset { @@ -34,6 +36,9 @@ object SparkConvertRDDtoDataset { val t = parser.get("targetPath") log.info(s"targetPath -> $t") + val filterRelation = parser.get("filterRelation") + log.info(s"filterRelation -> $filterRelation") + val entityPath = s"$t/entities" val relPath = s"$t/relation" val mapper = new ObjectMapper() @@ -94,28 +99,44 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") - val relationSemanticFilter = List( -// "cites", -// "iscitedby", - "merges", - "ismergedin", - "HasAmongTopNSimilarDocuments", - "IsAmongTopNSimilarDocuments" - ) + if (filterRelation != null && StringUtils.isNoneBlank(filterRelation)) { - val rddRelation = spark.sparkContext - .textFile(s"$sourcePath/relation") - .map(s => mapper.readValue(s, classOf[Relation])) - .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) - .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) - //filter OpenCitations relations - .filter(r => - r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => - "opencitations".equalsIgnoreCase(k.getValue) + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) ) + .filter(r => r.getSubRelType != null && r.getSubRelType.equalsIgnoreCase(filterRelation)) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } else { + + val relationSemanticFilter = List( + "merges", + "ismergedin", + "HasAmongTopNSimilarDocuments", + "IsAmongTopNSimilarDocuments" ) - .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) - spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + + val rddRelation = spark.sparkContext + .textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) + .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) + ) + .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) + spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") + } } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index 86d2f93c9c..f3b7246b1a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -321,4 +321,27 @@ public class PrepareResultProjectJobTest { 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); } + + @Test + void testMatchx() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index 4967ae5a53..7046b02c22 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Result; @@ -76,7 +77,11 @@ public class ResultLinkedToProjectTest { .getPath(); final String graphPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") .getPath(); SparkResultLinkedToProject.main(new String[] { @@ -84,20 +89,18 @@ public class ResultLinkedToProjectTest { "-outputPath", workingDir.toString() + "/preparedInfo", "-sourcePath", sourcePath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", graphPath + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc + JavaRDD tmp = sc .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Result.class)); - - Assertions.assertEquals(0, verificationDataset.count()); + Assertions.assertEquals(0, tmp.count()); } @@ -108,8 +111,12 @@ public class ResultLinkedToProjectTest { .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json") .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") + final String graphPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/preparedInfo") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath") .getPath(); SparkResultLinkedToProject.main(new String[] { @@ -117,20 +124,18 @@ public class ResultLinkedToProjectTest { "-outputPath", workingDir.toString() + "/preparedInfo", "-sourcePath", sourcePath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-graphPath", relationPath + "-graphPath", graphPath, + "-communityMapPath", communityMapPath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - JavaRDD tmp = sc + JavaRDD tmp = sc .textFile(workingDir.toString() + "/preparedInfo") - .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - org.apache.spark.sql.Dataset verificationDataset = spark - .createDataset(tmp.rdd(), Encoders.bean(Publication.class)); - - Assertions.assertEquals(1, verificationDataset.count()); + Assertions.assertEquals(1, tmp.count()); } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 477481c080..e9d739db28 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -5,10 +5,14 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults2; +// import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkGetFunderList; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.AfterAll; @@ -68,20 +72,19 @@ public class SplitPerFunderTest { void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext") .getPath(); SparkDumpFunderResults.main(new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-outputPath", workingDir.toString() + "/split", - "-sourcePath", sourcePath, - "-graphPath", sourcePath + "-sourcePath", sourcePath }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - // FP7 3 + // FP7 3 and H2020 3 JavaRDD tmp = sc .textFile(workingDir.toString() + "/split/EC_FP7") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); @@ -143,11 +146,6 @@ public class SplitPerFunderTest { .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(1, tmp.count()); - // CONICYT 0 - tmp = sc - .textFile(workingDir.toString() + "/split/CONICYTF") - .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); - Assertions.assertEquals(0, tmp.count()); - } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java new file mode 100644 index 0000000000..8cdb285e4b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectSubsetTest.java @@ -0,0 +1,125 @@ + +package eu.dnetlib.dhp.oa.graph.dump.projectssubset; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; + +public class ProjectSubsetTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static SparkSession spark; + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory( + eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()); + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectSubsetTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testAllNew() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/allnew/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(12, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(1, tmp.filter(p -> p.getId().substring(3, 15).equals("corda_______")).count()); + Assertions.assertEquals(40, sc.textFile(workingDir.toString() + "/projectIds").count()); + } + + @Test + void testMatchOne() throws Exception { + final String projectListPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/projectId") + .getPath(); + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/projectsubset/matchOne/projects") + .getPath(); + spark + .read() + .textFile(projectListPath) + .write() + .mode(SaveMode.Overwrite) + .text(workingDir.toString() + "/projectIds"); + ProjectsSubsetSparkJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/projects", + "-sourcePath", sourcePath, + "-projectListPath", workingDir.toString() + "/projectIds" + }); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/projects") + .map(item -> OBJECT_MAPPER.readValue(item, Project.class)); + Assertions.assertEquals(11, tmp.count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("aka_________")).count()); + Assertions.assertEquals(2, tmp.filter(p -> p.getId().substring(3, 15).equals("anr_________")).count()); + Assertions.assertEquals(4, tmp.filter(p -> p.getId().substring(3, 15).equals("arc_________")).count()); + Assertions.assertEquals(3, tmp.filter(p -> p.getId().substring(3, 15).equals("conicytf____")).count()); + Assertions.assertEquals(0, tmp.filter(p -> p.getId().substring(3, 15).equals("corda__h2020")).count()); + Assertions.assertEquals(39, sc.textFile(workingDir.toString() + "/projectIds").count()); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index f5cb86bfda..b75f626d61 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -122,6 +122,10 @@ class MappersTest { assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); + assertNotNull(p.getFulltext()); + assertEquals(1, p.getFulltext().size()); + assertEquals("https://oneecosystem.pensoft.net/article/13718/", p.getFulltext().get(0).getValue()); + // RESULT PROJECT List resultProject = list .stream() diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap new file mode 100644 index 0000000000..905cdabe92 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/communityMapPath/communityMap @@ -0,0 +1 @@ +{"ee":"SDSN - Greece","epos":"EPOS","enrmaps":"Energy Research","fet-h2020":"FET H2020","instruct":"Instruct-Eric","egi":"EGI Federation","euromarine":"Euromarine","covid-19":"COVID-19","dariah":"DARIAH EU","rda":"Research Data Alliance","clarin":"CLARIN","aginfra":"Agricultural and Food Sciences","risis":"RISI","fam":"Fisheries and Aquaculture Management","beopen":"Transport Research","elixir-gr":"ELIXIR GR","fet-fp7":"FET FP7","ifremer":"Ifremer","science-innovation-policy":"Science and Innovation Policy Studies","mes":"European Marine Scinece","oa-pg":"EC Post-Grant Open Access Pilot","ni":"Neuroinformatics","dh-ch":"Digital Humanities and Cultural Heritage"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/dataset similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump/orp rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/dataset diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/otherresearchproduct new file mode 100644 index 0000000000..e69de29bb2 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/funderresource/ext/project new file mode 100644 index 0000000000..f68cead77a --- /dev/null +++ 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Departamento de Ciencias Ambientales y Recursos Naturales","Universidad de Alicante. Centro Iberoamericano de la Biodiversidad","Biodiversidad y Biotecnología aplicadas a la Biología de la Conservación","Terrestrial Ecology (TE)"],"country":[{"code":"NL","label":"Netherlands","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"ES","label":"Spain","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2018-10-03T06:57:46.116Z","description":["Herbivory affects subsequent herbivores, mainly regulated by the phytohormones jasmonic (JA) and salicylic acid (SA). Additionally, organisms such as soil microbes belowground or parasitoids that develop inside their herbivorous hosts aboveground, can change plant responses to herbivory. However, it is not yet well known how organisms of trophic levels other than herbivores, below- and above-ground, alter the interactions between insect species sharing a host plant. Here, we investigated whether the parasitoid Aphidius colemani and different soil microbial communities (created through plant-soil feedbacks) affect the JA and SA signalling pathways in response to the aphid Myzus persicae and the thrips Frankliniella occidentalis, as well as subsequent thrips performance. Our results show that the expression of the JA-responsive gene CaPINII in sweet pepper was more suppressed by aphids than by parasitised aphids. However, parasitism did not affect the expression of CaPAL1, a biosynthetic gene of SA. Furthermore, aphid feeding enhanced thrips performance compared with uninfested plants, but this was not observed when aphids were parasitised. Soils where different plant species were previously grown, did not affect plant responses or the interaction between herbivores. Our study shows that members of the third trophic level can modify herbivore interactions by altering plant physiology.\nThis work and T.V.’s activities were supported by Spanish Ministry of Science and Innovation, (CGL2016-79054), the Open Technology Program of NWO (TTW-13848), and the STSM Cost Action FA1405 funded by the European Union. A.P. research activities were supported by the Netherlands Organisation for Scientific Research (NWO, project no. 870.15.080)."],"format":["application/pdf","application/octet-stream"],"id":"50|dedup_wf_001::01644aebfe64e809f593492e515bc070","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"hostedby":{"key":"10|opendoar____::e820a45f1dfc7b95282d10b6087e11c0","value":"Repositorio Institucional de la Universidad de Alicante"},"license":"Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. 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Computer Science and Artificial Intelligence Laboratory","Massachusetts Institute of Technology. Department of Mathematics","Lipson, Mark","Loh, Po-Ru","Berger, Bonnie"],"country":[{"code":"DZ","label":"Algeria","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}},{"code":"US","label":"United States","provenance":{"provenance":"Propagation of country to result collected from datasources of type institutional repositories","trust":"0.85"}}],"coverage":[],"dateofcollection":"2020-09-12T07:56:34.334Z","description":["Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.","National Science Foundation (U.S.). 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Zsigmond","name":"Anna","pid":{"id":{"scheme":"orcid","value":"0000-0002-3368-8863"}},"rank":1,"surname":"Zsigmond"}],"bestaccessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":[{"key":"10|openaire____::666894f04637d4dd1861ad117e1c4a66","value":"SNSF P3 Database"},{"key":"10|opendoar____::fc490ca45c00b1249bbe3554a4fdf6fb","value":"CERN Document Server"},{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID"},{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"}],"context":[{"code":"egi","label":"EGI Federation","provenance":[{"provenance":"Inferred by 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In this paper the first results from the proton–lead collision data taken in early 2013 are presented. The Z boson production cross section is measured in the muon decay channel in bins of transverse momentum and rapidity together with the forward–backward ratio. The W production is studied in the muon and electron decay channels and the differential cross sections, lepton-charge and forward–backward asymmetries are computed as a function of the lepton pseudorapidity. All results are compared with theory predictions with and without nuclear modification of the parton distribution functions showing hints of nuclear effects."],"format":[],"id":"50|dedup_wf_001::02cb7e7397a1f775e53ed38b38aba680","instance":[{"accessright":{"code":"c_14cb","label":"CLOSED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::666894f04637d4dd1861ad117e1c4a66","value":"SNSF P3 Database"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2014-01-01","refereed":"peerReviewed","type":"Conference object","url":["http://dx.doi.org/doi:10.1016/j.nuclphysa.2014.07.039"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::fc490ca45c00b1249bbe3554a4fdf6fb","value":"CERN Document 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prognostic accuracy in patients with disorders of consciousness. Due to the portability and relative inexpensiveness of electroencephalography, the N400 event-related potential component has been proposed as a clinically valid means to identify preserved linguistic function in non-communicative patients. Across three experiments, we show that changes in both stimuli and task demands significantly influence the probability of detecting statistically significant N400 effects — that is, the difference in N400 amplitudes caused by the experimental manipulation. In terms of task demands, passively heard linguistic stimuli were significantly less likely to elicit N400 effects than task-relevant stimuli. Due to the inability of the majority of patients with disorders of consciousness to follow task commands, the insensitivity of passive listening would impede the identification of residual language abilities even when such abilities exist. In terms of stimuli, passively heard normatively associated word pairs produced the highest detection rate of N400 effects (50% of the participants), compared with semantically-similar word pairs (0%) and high-cloze sentences (17%). This result is consistent with a prediction error account of N400 magnitude, with highly predictable targets leading to smaller N400 waves, and therefore larger N400 effects. Overall, our data indicate that non-repeating normatively associated word pairs provide the highest probability of detecting single-subject N400s during passive listening, and may thereby provide a clinically viable means of assessing residual linguistic function. We also show that more liberal analyses may further increase the detection-rate, but at the potential cost of increased false alarms.","Highlights • The N400 is a candidate marker of linguistic function after severe brain injury. • The probability of detecting N400s is dependent on task demands. • Passive listening is less sensitive than command-following. • The probability of detecting N400s is dependent on stimuli choices. • Word-pairs generated from association norms provide the highest sensitivity."],"format":["application/pdf"],"id":"50|dedup_wf_001::03d1b1b04480058e646b34c174e61082","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a","value":"NeuroImage: 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New polyethers, such as iubol (2), 22-hydroxy-15(28)- dehydrovenustatriol (3), 1,2-dehydropseudodehydrothyrsiferol (4), and secodehydrothyrsiferol (5) have been isolated and characterized from this alga. The structures were determined through the interpretation of NMR spectroscopic data and the relative configuration was proposed on the basis of NOESY spectrum and biogenetic considerations. All new compounds exhibited significant cytotoxic activity against a panel of cancer cell lines. © 2011 by the authors.","Financial support was provided by the grants MAREX (FP 7; KBBE-3-245137) (EU), CTQ2008-06754-C04-01 and SAF2008-02251 (MICINN); C2008000145 and EXMAR (ACISII); RD06/0020/1037 from Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, co-funded by the Fondo Europeo de Desarrollo Regional of the European Union, and Junta de Castilla y León (CSI052A11-2, and GR15-Experimental Therapeutics and Translational Oncology Program). 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The validity and utility of standard measures of childhood maltreatment requires clarification in order to inform the design of future studies investigating the mental health consequences of maltreatment. The present study assessed agreement between prospective informant-reports and retrospective self-reports of childhood maltreatment, as well as the comparative utility of both reports for predicting a range of psychiatric problems at age 18. Data were obtained from the Environmental Risk (E-Risk) Longitudinal Twin Study, a nationally-representative birth cohort of 2232 children followed to 18 years of age (with 93% retention). Childhood maltreatment was assessed in two ways: (i) prospective informant-reports from caregivers, researchers, and clinicians when children were aged 5, 7, 10 and 12; and (ii) retrospective self-reports of maltreatment experiences occurring up to age 12, obtained at age 18 using the Childhood Trauma Questionnaire. Participants were privately interviewed at age 18 concerning several psychiatric problems including depression, anxiety, self-injury, alcohol/cannabis dependence, and conduct disorder. There was only slight to fair agreement between prospective and retrospective reports of childhood maltreatment (all Kappa's ≤ 0.31). Both prospective and retrospective reports of maltreatment were associated with age-18 psychiatric problems, though the strongest associations were found when maltreatment was retrospectively self-reported. These findings indicate that prospective and retrospective reports of childhood maltreatment capture largely non-overlapping groups of individuals. Young adults who recall being maltreated have a particularly elevated risk for psychopathology."],"format":["application/pdf","text"],"id":"50|dedup_wf_001::085f9efc74e1192abca87031fb573d70","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research Portal"},"hostedby":{"key":"10|opendoar____::566a9968b43628588e76be5a85a0f9e8","value":"King's Research 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Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas.\r\nUsing transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium).\r\nNative soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.\r\nThe ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses."],"format":[],"id":"50|dedup_wf_001::09e54cbad6670d8f40a7de2704e2d2a4","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"license":"http://doi.wiley.com/10.1002/tdm_license_1.1","publicationdate":"2018-02-09","refereed":"UNKNOWN","type":"Article","url":["https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fnph.15014","http://onlinelibrary.wiley.com/wol1/doi/10.1111/nph.15014/fullpdf","http://dx.doi.org/10.1111/nph.15014"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.15014"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|issn___print::35ee75a5ad42581d604be113a8f56427","value":"New Phytologist"},"refereed":"UNKNOWN","type":"Article","url":["https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15014","https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014","http://onlinelibrary.wiley.com/doi/10.1111/nph.15014/abstract","https://aperto.unito.it/handle/2318/1660820","https://academic.microsoft.com/#/detail/2793208206"]},{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"hostedby":{"key":"10|opendoar____::89fcd07f20b6785b92134bd6c1d0fa42","value":"Archivio Istituzionale"},"publicationdate":"2018-01-01","refereed":"UNKNOWN","type":"Article","url":["http://hdl.handle.net/2318/1660820"]},{"collectedfrom":{"key":"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254","value":"Datacite"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2018-12-01","refereed":"UNKNOWN","type":"Other literature type","url":["http://dx.doi.org/10.1111/nph.15014"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Native soils with their microbiotas elicit a state of alert in tomato plants","originalId":["10.1111/nph.15014","2793208206","oai:iris.unito.it:2318/1660820"],"pid":[{"scheme":"doi","value":"10.1111/nph.15014"},{"scheme":"pmid","value":"29424928"}],"projects":[{"acronym":"TomRes","code":"727929","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::94c4a066401e22002c4811a301bb4655","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"A NOVEL AND INTEGRATED APPROACH TO INCREASE MULTIPLE AND COMBINED STRESS TOLERANCE IN PLANTS USING TOMATO AS A MODEL"}],"publicationdate":"2018-12-01","publisher":"Wiley","subjects":[{"subject":{"scheme":"keywords","value":"Plant Science"}},{"subject":{"scheme":"keywords","value":"Physiology"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"UNKNOWN","value":"Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"food and beverages"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.891"},"subject":{"scheme":"mesheuropmc","value":"fungi"}},{"provenance":{"provenance":"Inferred by OpenAIRE","trust":"0.8739"},"subject":{"scheme":"mesheuropmc","value":"complex mixtures"}}],"type":"publication"} +{"author":[{"fullname":"K.P. Moustris","name":"K. P.","rank":1,"surname":"Moustris"},{"fullname":"D. Zafirakis","name":"D.","rank":2,"surname":"Zafirakis"},{"fullname":"K.A. Kavvadias","name":"K. A.","rank":3,"surname":"Kavvadias"},{"fullname":"J.K. Kaldellis","name":"J. 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To this end, the main objective of this work is the prognosis of the mean, maximum and minimum hourly wind power (WP) 8hours ahead. For this purpose, Artificial Neural Networks (ANN) modeling is applied. For the appropriate training of the developed ANN models hourly meteorological data are used. These data have been recorded by a meteorological mast in Tilos Island, Greece.\n\nFor the evaluation of the developed ANN forecasting models proper statistical evaluation indices are used. According to the results, the coefficient of the determination ranges from 0.285 up to 0.768 (mean hourly WP), from 0.227 up to 0.798 (maximum hourly WP) and from 0.025 up to 0.398 (minimum hourly WP). Furthermore, the proposed forecasting methodology shows that is able to give sufficient and adequate prognosis of WP by a wind turbine in a specific location 8 hours ahead. This will be a useful tool for the operator of a RES system in order to achieve a better monitoring and a better management of the whole system."],"format":[],"id":"50|dedup_wf_001::0a6525f420fd1f922125c3a1a280c8df","instance":[{"accessright":{"code":"c_16ec","label":"RESTRICTED","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"publicationdate":"2017-02-23T20:11:53Z","refereed":"UNKNOWN","type":"Conference object","url":["http://digital-library.theiet.org/content/conferences/10.1049/cp.2016.1094?crawler=true","http://dx.doi.org/10.1049/cp.2016.1094"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|openaire____::8ac8380272269217cb09a928c8caa993","value":"UnpayWall"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"license":"cc-by","refereed":"UNKNOWN","type":"Conference object","url":["https://zenodo.org/record/887339/files/Wind%20power%20forecasting%20using%20historical%20data%20and%20artificial%20neural%20networks%20modeling.pdf"]},{"collectedfrom":{"key":"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a","value":"Microsoft Academic Graph"},"hostedby":{"key":"10|openaire____::55045bd2a65019fd8e6741a755395c8c","value":"Unknown Repository"},"refereed":"UNKNOWN","type":"Conference object","url":["http://digital-library.theiet.org/content/conferences/10.1049/cp.2016.1094","https://core.ac.uk/display/144851191","http://jglobal.jst.go.jp/public/20090422/201702260673071390","https://academic.microsoft.com/#/detail/2590295725"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::358aee4cc897452c00244351e4d91f69","value":"ZENODO"},"hostedby":{"key":"10|opendoar____::358aee4cc897452c00244351e4d91f69","value":"ZENODO"},"license":"http://creativecommons.org/licenses/by/4.0/legalcode","publicationdate":"2016-11-07","refereed":"UNKNOWN","type":"Conference object","url":["https://zenodo.org/record/887339"]}],"language":{"code":"und","label":"Undetermined"},"lastupdatetimestamp":1603727328518,"maintitle":"Wind power forecasting using historical data and artificial neural networks modeling","originalId":["10.1049/cp.2016.1094","2590295725","oai:zenodo.org:887339"],"pid":[{"scheme":"doi","value":"10.1049/cp.2016.1094"}],"projects":[{"acronym":"TILOS","code":"646529","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|corda__h2020::64c901e621f90b9a38badb1d78902205","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Technology Innovation for the Local Scale, Optimum Integration of Battery Energy Storage"}],"publicationdate":"2016-11-07","publisher":"Institution of Engineering and Technology","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"Wind Power, Forecasting, Artificial Neural Networks"}}],"type":"publication"} +{"author":[{"fullname":"Juan M. 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The experimental evapotranspiration values calculated represent the maximum value in absence of stress, so the resulting crop coefficients should be used with some caution. 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. En conclusión, la depresión y el estrés diario parecen ser contribuidores importantes al círculo vicioso de la perpetuación de los síntomas SII."],"format":["application/pdf"],"id":"50|dedup_wf_001::054ea3bc3ccc386d150d900776e1070d","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"hostedby":{"key":"10|opendoar____::2e3d2c4f33a7a1f58bc6c81cacd21e9c","value":"Repository of the University of Rijeka, Faculty of Humanities and Social Sciences"},"license":"http://creativecommons.org/licenses/by/4.0/","publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["https://repository.ffri.uniri.hr/islandora/object/ffri:1182","https://urn.nsk.hr/urn:nbn:hr:186:701987","https://repository.ffri.uniri.hr/islandora/object/ffri:1182/datastream/FILE0"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"hostedby":{"key":"10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0","value":"HRČAK - Portal of scientific journals of Croatia"},"publicationdate":"2016-01-01","refereed":"UNKNOWN","type":"Other literature type","url":["https://hrcak.srce.hr/156331","https://hrcak.srce.hr/file/230444"]},{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"},"hostedby":{"key":"10|doajarticles::23738aeeb586d9f9b652c75aaff54dd4","value":"Psychological Topics"},"publicationdate":"2016-04-01","refereed":"UNKNOWN","type":"Article","url":["http://pt.ffri.hr/index.php/pt/article/view/317","https://doaj.org/toc/1332-0742"]}],"language":{"code":"eng","label":"English"},"lastupdatetimestamp":1603727328518,"maintitle":"The role of stress in IBS symptom severity","originalId":["oai:repository.ffri.uniri.hr:ffri_1182","oai:hrcak.srce.hr:156331","oai:doaj.org/article:4394c5a4f62849ffac7ea485a91540a3"],"pid":[],"projects":[{"code":"009-0092660-2655","funder":{"jurisdiction":"HR","name":"Ministry of Science, Education and Sports of the Republic of Croatia (MSES)","shortName":"MZOS"},"id":"40|irb_hr______::ad496254144c27606e4058841e060fa0","provenance":{"provenance":"Harvested","trust":"0.900000000000000022"},"title":"Psychosomatic aspects of chronic functional and inflammatory bowel diseases"}],"publicationdate":"2016-04-01","subjects":[{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"irritable bowel syndrome"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"symptom severity"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"daily stress"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"depression"}},{"provenance":{"provenance":"Harvested","trust":"0.9"},"subject":{"scheme":"keyword","value":"DRUŠTVENE ZNANOSTI. 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central problem for the function and manufacture of materials where performance relies on nanoscale structure is to control the compatibility and interactions of the building blocks. 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Ce qui nous frappe en premier lieu dans le roman de Melchior Mbonimpa, Le Totem des Baranda, c'est l'efficacité de sa fonction didactique. Le livre est porteur d'un message, d'une vision sur l'histoire de l'Afrique des Grands Lacs qu'on rencontre rarement dans l'actualité ou l'histoire immédiate que nous livrent les médias.

Cette thèse se penchera sur un aspect de ce roman qui a particulièrement attiré notre attention: la représentation de la résistance à travers l'affirmation identitaire des personnages féminins. Dans notre analyse de ce thème, nous accordons une grande importance au contexte socioculturel et à l'imaginaire collectif qui nourrissent l'auteur et dans lesquels s'inscrivent ses personnages. L'étude soulignera la fonction sociale de l'écrivain et relèvera la contribution de la fiction à la culture africaine. Nous mettrons en évidence les positions idéologiques de l'auteur et le message de sensibilisation qu'il adresse à diverses catégories de lecteurs: ceux qui se trouvent en Afrique, les Africains de la diaspora, et les lecteurs non-Africains qui s'intéressent à son œuvre. Cette orientation idéologique affecte évidemment la manière dont s'exprime la résistance des pnncIpaux personnages féminins du roman. Elle détermine la place que cette fiction accorde à la femme, et qui correspond sans doute à la place que, selon les souhaits de l'auteur, la femme devrait occuper dans le contexte culturel africain. Notre étude insiste aussi sur le fait que dans ce roman, la modernité se nourrit de la culture traditionnelle et ne renie pas les valeurs du passé.

Ainsi, le parcours narratif montre que dans leur résistance, les héroïnes de la généalogie vivent à leur époque, mais chacune porte plus loin une mission transmise par les précédentes.

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The superconducting transition in the magnetic resistance of members of the family of bismuth based high temperature superconductors was investigated. Measurements were performed in magnetic fields up to 1.7 T. Small current densities ranging from 0.03 A/cm² to 3.0 A/cm² were applied. The resistivity of Bi₂Sr₂CaCu₂Ox single crystals was analyzed in terms of the thermally activated flux flow expression, ρ =ρ₀U/T exp(-U/T) where T is the temperature. It was found that the activation energy was given by Uα(Hsinθ)^(⁻α) where α≈1/3 and that the prefactor had the form, ρ₀Hsinθ, where H was the applied field and θ the angle of the field with respect to the CuO₂ planes. Results demonstrated that dissipation could be accounted for by the motion of two-dimensional vortices whose density is given by the field, Hsinθ, projected on the CuO₂ planes. Measurements of the resistivity and current dependent resistivity were performed with two Sn-doped and two Sb-doped polycrystalline Bi(1.7)Pb(0.3)Sr₂Ca₂Cu₃O(y) samples. Features in the temperature derivative of the resistivity curves were associated with the presence of a superconducting transition between superconducting grains, coupled by weak links with a distribution of critical currents and critical temperatures, and the superconducting transition within grains. The transition between grains was more strongly suppressed in temperature with the application of a magnetic field in samples with weaker coupling between grains. The presence of a transition in a magnetic field due to weak links between grains was verified at 77 K by the observation of a current dependent resistivity in a magnetic field. Measurements of a Bi₂Sr₂CaCu₂Ox diffusion grown thick film ring were done. The transverse voltage, the voltage at the centre of a 120 μm thick branch with respect to the centre of a 76 μm thick branch, was measured. A higher critical temperature from the presence of more texturing in the 76 μm branch as determined by separate resistivity, x-ray and scanning electron microscopy measurements was consistent with the measurement of a crossover from a negative to positive transverse voltage as the temperature of the sample went through its superconducting transition.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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This study examines Leonard Cohen's novel Beautiful Losers through the lenses of allegorical and authorial theories to appreciate how the novel uses allegorical techniques to code into symbolic terms an exploration of the polysemous nature of the word ''translation.'' The first chapter studies the stylistic and conceptual dimensions of allegory as a literary genre - as critics like Northrop Frye, Angus Fletchet, and Maureen Quilligan help to define it - while arguing that Cohen's novel is consciously allegorical, challenging readers to interpret what it \"means,\" or may mean. The second chapter performs an intensive re-reading of Beautiful Losers, examining how the novel uses complex systems of verbal play (particularly puns) to coordinate a reunification of various dichotomies historical \"reality\"/imaginative myth, secularity/spirituality, enslavement/sanctification, among others - employed throughout the text. The thesis concludes that the novel is perpetually playing with various types of translation (spiritual, linguistic, physical, and so forth), affirming the need for emotionally-charged, devotional forms of expression (like song and prayer) over more clinical attempts to reorder or recreate the world and its inhabitants. Ultimately, this discussion argues that an understanding of the allegorical dimensions of Beautiful Losers may illuminate how Cohen's other works (particularly his songs) may be studied as attempts to associate word with voice, to emphasize the process of expression (translation) rather than just the finished product.

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+40|nsf_________::56297da8b472a4be8ac3f09af813c9f6 +40|nsf_________::6b6dc3398eeebb3de1ab66e6eb8c5cb3 +40|nih_________::93289a36ebffb0bee3d6b01c6fc0a3d6 +40|nih_________::6c3b00dd4ae9d43d6630ff18f189ebae +40|nih_________::1d983a87768f13bc8377b1b7d17290a2 +40|nih_________::c3b56e91859b114644c1403e892eb80f +40|rcuk________::c1e15330fc7956063652f9c06e584548 \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index 27128138cd..b34ec96934 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -999,17 +999,11 @@ public class XmlRecordFactory implements Serializable { private List measuresAsXml(List measures) { return measures .stream() - .flatMap( - m -> m - .getUnit() - .stream() - .map( - u -> Lists - .newArrayList( - new Tuple2<>("id", m.getId()), - new Tuple2<>("key", u.getKey()), - new Tuple2<>("value", u.getValue()))) - .map(l -> XmlSerializationUtils.asXmlElement("measure", l))) + .map(m -> { + List> l = Lists.newArrayList(new Tuple2<>("id", m.getId())); + m.getUnit().forEach(kv -> l.add(new Tuple2<>(kv.getKey(), kv.getValue()))); + return XmlSerializationUtils.asXmlElement("measure", l); + }) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index f4763618b5..92d9f497fb 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -73,11 +73,20 @@ public class XmlRecordFactoryTest { assertEquals("EUR", doc.valueOf("//processingchargecurrency/text()")); assertEquals( - "1.00889953098e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@value")); + "5.06690394631e-09", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@score")); assertEquals( - "30.6576853333", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@value")); + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@class")); + assertEquals( - "4.62970429725e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@value")); + "0.0", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@score")); + assertEquals( + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@class")); + + assertEquals( + "3.11855618382e-09", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@score")); + assertEquals( + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@class")); + } @Test diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index 2c52ce269f..41ced45ae4 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -5,7 +5,37 @@ "unit": [ { "key": "score", - "value": "1.00889953098e-08" + "value": "5.06690394631e-09", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] }, @@ -14,7 +44,37 @@ "unit": [ { "key": "score", - "value": "30.6576853333" + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] }, @@ -23,7 +83,115 @@ "unit": [ { "key": "score", - "value": "4.62970429725e-08" + "value": "3.11855618382e-09", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ] + }, + { + "id": "influence_alt", + "unit": [ + { + "key": "score", + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ] + }, + { + "id": "impulse", + "unit": [ + { + "key": "score", + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] } diff --git a/pom.xml b/pom.xml index 54070f654c..973bc37732 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.12.0] + [2.12.2-SNAPSHOT] [4.0.3] [6.0.5] [3.1.6]